{"group":{"id":1,"name":"Community","lockable":false,"created_at":"2012-01-18T18:02:15.000Z","updated_at":"2025-12-14T01:33:56.000Z","description":"Problems submitted by members of the MATLAB Central community.","is_default":true,"created_by":161519,"badge_id":null,"featured":false,"trending":false,"solution_count_in_trending_period":0,"trending_last_calculated":"2025-12-14T00:00:00.000Z","image_id":null,"published":true,"community_created":false,"status_id":2,"is_default_group_for_player":false,"deleted_by":null,"deleted_at":null,"restored_by":null,"restored_at":null,"description_opc":null,"description_html":null,"published_at":null},"problems":[{"id":2513,"title":"Genome decoding","description":"Inspired by a question on the answer forum:\r\n\r\nYou are given a matrix of 8-bit integers which encodes a genome. Each integer can be converted into a sequence by converting it first to binary and then converting bit pairs using the rule A = 00, C = 01, T = 10, G = 11. \r\nFor example, 177 -\u003e 10110001 -\u003e TGAC. \r\n\r\nConvert the matrix into a cell array of sequences.\r\n\r\nstr2num and regexp not allowed.","description_html":"\u003cp\u003eInspired by a question on the answer forum:\u003c/p\u003e\u003cp\u003eYou are given a matrix of 8-bit integers which encodes a genome. Each integer can be converted into a sequence by converting it first to binary and then converting bit pairs using the rule A = 00, C = 01, T = 10, G = 11. \r\nFor example, 177 -\u0026gt; 10110001 -\u0026gt; TGAC.\u003c/p\u003e\u003cp\u003eConvert the matrix into a cell array of sequences.\u003c/p\u003e\u003cp\u003estr2num and regexp not allowed.\u003c/p\u003e","function_template":"function [sequences] = decode_genome(genome)\r\n sequences = 'ACTG';\r\nend","test_suite":"%%\r\nuser_solution = fileread('decode_genome.m');\r\nassert(isempty(strfind(user_solution,'regexp')));\r\nassert(isempty(strfind(user_solution,'str2num')));\r\n\r\n%%\r\ngenome = [\r\n 228 24 40 36 167\r\n 231 71 248 107 9\r\n 32 140 245 234 217\r\n 233 0 124 202 239\r\n 161 247 204 255 173];\r\nsequences = {\r\n 'GTCA' 'ACTA' 'ATTA' 'ATCA' 'TTCG'\r\n 'GTCG' 'CACG' 'GGTA' 'CTTG' 'AATC'\r\n 'ATAA' 'TAGA' 'GGCC' 'GTTT' 'GCTC'\r\n 'GTTC' 'AAAA' 'CGGA' 'GATT' 'GTGG'\r\n 'TTAC' 'GGCG' 'GAGA' 'GGGG' 'TTGC'};\r\nassert(isequal(sequences, decode_genome(genome)));\r\n\r\n%%\r\ngenome = [1 4 16 64; 234 186 174 171];\r\nsequences = {'AAAC' 'AACA' 'ACAA' 'CAAA'; 'GTTT' 'TGTT' 'TTGT' 'TTTG'};\r\nassert(isequal(sequences, decode_genome(genome)));\r\n\r\n%%\r\ngenome = [228 225 216 210 198 201 180 177 156 147 135 141 108 99 120 114 78 75 39 45 27 30 54 57]';\r\nsequences = {'GTCA' 'GTAC' 'GCTA' 'GCAT' 'GACT' 'GATC' 'TGCA' 'TGAC' 'TCGA' 'TCAG' 'TACG' 'TAGC' 'CTGA' 'CTAG' 'CGTA' 'CGAT' 'CAGT' 'CATG' 'ATCG' 'ATGC' 'ACTG' 'ACGT' 'AGCT' 'AGTC'}';\r\nassert(isequal(sequences, decode_genome(genome)));","published":true,"deleted":false,"likes_count":2,"comments_count":0,"created_by":999,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":68,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":32,"created_at":"2014-08-17T10:20:31.000Z","updated_at":"2026-03-19T20:07:27.000Z","published_at":"2014-08-17T10:20:31.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eInspired by a question on the answer forum:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eYou are given a matrix of 8-bit integers which encodes a genome. Each integer can be converted into a sequence by converting it first to binary and then converting bit pairs using the rule A = 00, C = 01, T = 10, G = 11. For example, 177 -\u0026gt; 10110001 -\u0026gt; TGAC.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eConvert the matrix into a cell array of sequences.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003estr2num and regexp not allowed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":912,"title":"Genome Sequence 002: Introductory DNA Sequencing (Flipped Segments)","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssTACAGGTACCGGssss Middle\r\nsssssGGCCATGGACATssss Middle Reversed\r\nssssssssssssGACATTACG\r\nGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\r\nSegments may be flipped (Genome_002 change)\r\nLength of each segment - 48\r\nSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\nAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order will be scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\r\nExample: [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\r\nFuture: Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 727.2px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.6px; transform-origin: 407px 363.6px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 367px 8px; transform-origin: 367px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssTACAGGTACCGGssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 148px 8.5px; transform-origin: 148px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssGGCCATGGACATssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 60px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 60px 8.5px; \"\u003eMiddle Reversed\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 384px 8px; transform-origin: 384px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 155px 8px; transform-origin: 155px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be flipped (Genome_002 change)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 241px 8px; transform-origin: 241px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 324px 8px; transform-origin: 324px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order will be scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 184px 8px; transform-origin: 184px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 317px 8px; transform-origin: 317px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n G=[];\r\nend","test_suite":"%%\r\ntic\r\nL=4176; % 1040 Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n% Flip random segments\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":5,"test_suite_updated_at":"2021-07-16T14:47:06.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-08-15T19:14:39.000Z","updated_at":"2021-07-16T14:47:06.000Z","published_at":"2012-10-01T03:42:15.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssTACAGGTACCGGssss Middle\\nsssssGGCCATGGACATssss Middle Reversed\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be flipped (Genome_002 change)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":863,"title":"Genome Sequence 001: Introductory DNA Sequencing","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. \u003chttp://en.wikipedia.org/wiki/Genome DNA Sequencing\u003e and the \u003chttp://en.wikipedia.org/wiki/Shotgun_sequencing Shot Gun Method\u003e will be naively simplified into Cody Challenges. \u003chttp://en.wikipedia.org/wiki/Genome_sequence Genome sizes\u003e is another interesting wiki page.\r\n\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches. \r\n\r\n*Example:* G = ACGTCGGCCATGGACATTACG\r\n\r\nGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\r\n\r\n ACGTCGGCCATGGACATTACG\r\n ACGTCGGCCAsssssssssss\r\n sssssGGCCATGGACATssss\r\n ssssssssssssGACATTACG\r\n\r\n\r\n\r\nGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\r\n\r\n# Length of each segment - 48\r\n# Segments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\n# All segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\n# Segments read left to right (no flips)\r\n# No errors in the segments\r\n# Genome is random (No duplicate starts or ends for 16 symbols of segments)\r\n# Segments will be scrambled\r\n\r\n*Input:* segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\n\r\n*Output:* Gout, Genome vector of values [0,1,2,3]\r\n\r\n*Example:* [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\r\n\r\n*Future:* Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)","description_html":"\u003cp\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing. \u003ca href=\"http://en.wikipedia.org/wiki/Genome\"\u003eDNA Sequencing\u003c/a\u003e and the \u003ca href=\"http://en.wikipedia.org/wiki/Shotgun_sequencing\"\u003eShot Gun Method\u003c/a\u003e will be naively simplified into Cody Challenges. \u003ca href=\"http://en.wikipedia.org/wiki/Genome_sequence\"\u003eGenome sizes\u003c/a\u003e is another interesting wiki page.\u003c/p\u003e\u003cp\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e G = ACGTCGGCCATGGACATTACG\u003c/p\u003e\u003cp\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003eACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssGGCCATGGACATssss\r\nssssssssssssGACATTACG\r\n\u003c/pre\u003e\u003cp\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/p\u003e\u003col\u003e\u003cli\u003eLength of each segment - 48\u003c/li\u003e\u003cli\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/li\u003e\u003cli\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/li\u003e\u003cli\u003eSegments read left to right (no flips)\u003c/li\u003e\u003cli\u003eNo errors in the segments\u003c/li\u003e\u003cli\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/li\u003e\u003cli\u003eSegments will be scrambled\u003c/li\u003e\u003c/ol\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Gout, Genome vector of values [0,1,2,3]\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/p\u003e\u003cp\u003e\u003cb\u003eFuture:\u003c/b\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/p\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n G=[];\r\nend","test_suite":"tic\r\nL=4176; % 1040 Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":6,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":7,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-24T19:18:06.000Z","updated_at":"2012-10-01T00:04:58.000Z","published_at":"2012-10-01T00:04:58.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Shotgun_sequencing\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome_sequence\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e G = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssGGCCATGGACATssss\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments read left to right (no flips)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":797,"title":"Genome Sequence 003R: Sequence DNA of random positioned and flipped segments","description":"This is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments. DNA Sequencing is naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssGCCATGGACATCsssss Middle Rev\r\nssssCTACAGGTACCGsssss Middle flipped\r\nssssssssssssGACATTACG\r\nGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\r\nSegments may be reversed (Change from 003)\r\nSegments start at random positions\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 726.633px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.317px; transform-origin: 407px 363.317px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 341px 8px; transform-origin: 341px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 133.5px 8px; transform-origin: 133.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 368.5px 8px; transform-origin: 368.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 128px 8.5px; transform-origin: 128px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssGCCATGGACATCsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 40px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 40px 8.5px; \"\u003eMiddle Rev\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 144px 8.5px; transform-origin: 144px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 56px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 56px 8.5px; \"\u003eMiddle flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 382px 8px; transform-origin: 382px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 163.467px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 81.7333px; transform-origin: 391px 81.7333px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 148.5px 8px; transform-origin: 148.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be reversed (Change from 003)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 111.5px 8px; transform-origin: 111.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 324.5px 8px; transform-origin: 324.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 84px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 42px; text-align: left; transform-origin: 384px 42px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 355.5px 8px; transform-origin: 355.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003R(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=563*17;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2021-07-16T14:52:10.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-06-27T17:37:02.000Z","updated_at":"2021-07-16T14:52:10.000Z","published_at":"2012-10-07T22:51:12.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssGCCATGGACATCsssss Middle Rev\\nssssCTACAGGTACCGsssss Middle flipped\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be reversed (Change from 003)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":969,"title":"Genome Sequence 003: DNA Sequence with random positioned segments","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssCTACAGGTACCGsssss Middle\r\nssssssssssssGACATTACG\r\nGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\r\nSegments start at random positions (Genome_003 change from 001)\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 706.767px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 353.383px; transform-origin: 407px 353.383px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 366.5px 8px; transform-origin: 366.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 81.7333px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 40.8667px; transform-origin: 404px 40.8667px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 217px 8px; transform-origin: 217px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions (Genome_003 change from 001)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 250px 8px; transform-origin: 250px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 345.5px 8px; transform-origin: 345.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=1024;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":"2021-07-16T14:46:09.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-10-03T04:17:33.000Z","updated_at":"2025-05-05T20:24:45.000Z","published_at":"2012-10-03T04:47:11.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssCTACAGGTACCGsssss Middle\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions (Genome_003 change from 001)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":811,"title":"Genome Sequence 004: Long 3rd Generation Segment Correction","description":"The Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by \u003chttp://www.pacificbiosciences.com/ PacBio\u003e. The \u003chttp://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar Assemblathon Genome Contest\u003e led the team of Phillippy, Koren and Jarvis to successfully \u003chttp://www.sciencedaily.com/releases/2012/07/120702210229.htm Sequence Parrot DNA\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\r\n\r\nThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u003c1% error rate. Jarvis and his team combined this data to achieve \u003c 0.1% error rate.\r\n\r\nGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\r\n\r\n*Input:* \r\n\r\nCall 1: empty array, segment Width, Flag=0\r\n\r\nCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\r\n\r\n*Output:* \r\n\r\nCall 1: empty vector, Number of Requested Vectors\r\n\r\nCall 2: Corrected DNA vector, Number of Requested Vectors\r\n\r\n*Score:* Number of N vectors used to produce correct vector for w=1024 case\r\n\r\nThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\r\n\r\nThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\r\n\r\nThe response to the second call is the fixed DNA sequence, vector of width w.\r\n\r\n*example:*\r\nFirst call return : N=3\r\n\r\n 01230123111122223333 Truth\r\n Input example\r\n 01232123112122221332 Injected errors\r\n 01130123111122123323\r\n 11230133121122223333\r\n\r\n Output: \r\n 01230123111122223333 Truth, hopefully\r\n\r\n\r\nThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned. \r\n\r\nThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\r\n\r\nFollow-Up Challenges: Sample Data from the PacBio site for \u003chttp://www.cbcb.umd.edu/software/PBcR/ Lambda Phage\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\r\n","description_html":"\u003cp\u003eThe Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by \u003ca href=\"http://www.pacificbiosciences.com/\"\u003ePacBio\u003c/a\u003e. The \u003ca href=\"http://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar\"\u003eAssemblathon Genome Contest\u003c/a\u003e led the team of Phillippy, Koren and Jarvis to successfully \u003ca href=\"http://www.sciencedaily.com/releases/2012/07/120702210229.htm\"\u003eSequence Parrot DNA\u003c/a\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\u003c/p\u003e\u003cp\u003eThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u0026lt;1% error rate. Jarvis and his team combined this data to achieve \u0026lt; 0.1% error rate.\u003c/p\u003e\u003cp\u003eGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\u003c/p\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e\u003c/p\u003e\u003cp\u003eCall 1: empty array, segment Width, Flag=0\u003c/p\u003e\u003cp\u003eCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e\u003c/p\u003e\u003cp\u003eCall 1: empty vector, Number of Requested Vectors\u003c/p\u003e\u003cp\u003eCall 2: Corrected DNA vector, Number of Requested Vectors\u003c/p\u003e\u003cp\u003e\u003cb\u003eScore:\u003c/b\u003e Number of N vectors used to produce correct vector for w=1024 case\u003c/p\u003e\u003cp\u003eThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\u003c/p\u003e\u003cp\u003eThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\u003c/p\u003e\u003cp\u003eThe response to the second call is the fixed DNA sequence, vector of width w.\u003c/p\u003e\u003cp\u003e\u003cb\u003eexample:\u003c/b\u003e\r\nFirst call return : N=3\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003e01230123111122223333 Truth\r\nInput example\r\n01232123112122221332 Injected errors\r\n01130123111122123323\r\n11230133121122223333\r\n\u003c/pre\u003e\u003cpre class=\"language-matlab\"\u003eOutput: \r\n01230123111122223333 Truth, hopefully\r\n\u003c/pre\u003e\u003cp\u003eThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned.\u003c/p\u003e\u003cp\u003eThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\u003c/p\u003e\u003cp\u003eFollow-Up Challenges: Sample Data from the PacBio site for \u003ca href=\"http://www.cbcb.umd.edu/software/PBcR/\"\u003eLambda Phage\u003c/a\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\u003c/p\u003e","function_template":"function [M_fix,N]=PacBio_fix(M,w,flag)\r\n% 1st Call\r\n% M is empty\r\n% w is width of segment\r\n% flag is 0\r\n% Ouput is N, the number of segments requested to fix the segment\r\n% 2nd Call\r\n% M is an Nxw array of values [0:3]\r\n\r\n M_fix=[];\r\n N=1; % needed for 2nd call with flag==1\r\n if flag==0 % Requested number of Segments\r\n N=1;\r\n return;\r\n end\r\n\r\nM_fix=M(1,:);\r\n\r\n\r\nend","test_suite":"%%\r\nfeval(@assignin,'caller','score',0);\r\n%%\r\nM=[];\r\nflag=0;\r\nw=100;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n%%\r\nM=[];\r\nflag=0;\r\nw=6144;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n\r\n%%\r\n% Size Performance is based on w=1024 case\r\nM=[];\r\nflag=0;\r\nw=1024;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,not_N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n\r\nfeval(@assignin,'caller','score',min(20,N));\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":0,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2012-10-08T02:30:34.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-01T05:26:57.000Z","updated_at":"2012-10-08T02:40:09.000Z","published_at":"2012-10-08T02:29:50.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.pacificbiosciences.com/\\\"\u003e\u003cw:r\u003e\u003cw:t\u003ePacBio\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e. The\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eAssemblathon Genome Contest\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e led the team of Phillippy, Koren and Jarvis to successfully\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.sciencedaily.com/releases/2012/07/120702210229.htm\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eSequence Parrot DNA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u0026lt;1% error rate. Jarvis and his team combined this data to achieve \u0026lt; 0.1% error rate.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 1: empty array, segment Width, Flag=0\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 1: empty vector, Number of Requested Vectors\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 2: Corrected DNA vector, Number of Requested Vectors\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eScore:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Number of N vectors used to produce correct vector for w=1024 case\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe response to the second call is the fixed DNA sequence, vector of width w.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eexample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e First call return : N=3\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[01230123111122223333 Truth\\nInput example\\n01232123112122221332 Injected errors\\n01130123111122123323\\n11230133121122223333\\n\\nOutput: \\n01230123111122223333 Truth, hopefully]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eFollow-Up Challenges: Sample Data from the PacBio site for\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.cbcb.umd.edu/software/PBcR/\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eLambda Phage\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"}],"problem_search":{"errors":[],"problems":[{"id":2513,"title":"Genome decoding","description":"Inspired by a question on the answer forum:\r\n\r\nYou are given a matrix of 8-bit integers which encodes a genome. Each integer can be converted into a sequence by converting it first to binary and then converting bit pairs using the rule A = 00, C = 01, T = 10, G = 11. \r\nFor example, 177 -\u003e 10110001 -\u003e TGAC. \r\n\r\nConvert the matrix into a cell array of sequences.\r\n\r\nstr2num and regexp not allowed.","description_html":"\u003cp\u003eInspired by a question on the answer forum:\u003c/p\u003e\u003cp\u003eYou are given a matrix of 8-bit integers which encodes a genome. Each integer can be converted into a sequence by converting it first to binary and then converting bit pairs using the rule A = 00, C = 01, T = 10, G = 11. \r\nFor example, 177 -\u0026gt; 10110001 -\u0026gt; TGAC.\u003c/p\u003e\u003cp\u003eConvert the matrix into a cell array of sequences.\u003c/p\u003e\u003cp\u003estr2num and regexp not allowed.\u003c/p\u003e","function_template":"function [sequences] = decode_genome(genome)\r\n sequences = 'ACTG';\r\nend","test_suite":"%%\r\nuser_solution = fileread('decode_genome.m');\r\nassert(isempty(strfind(user_solution,'regexp')));\r\nassert(isempty(strfind(user_solution,'str2num')));\r\n\r\n%%\r\ngenome = [\r\n 228 24 40 36 167\r\n 231 71 248 107 9\r\n 32 140 245 234 217\r\n 233 0 124 202 239\r\n 161 247 204 255 173];\r\nsequences = {\r\n 'GTCA' 'ACTA' 'ATTA' 'ATCA' 'TTCG'\r\n 'GTCG' 'CACG' 'GGTA' 'CTTG' 'AATC'\r\n 'ATAA' 'TAGA' 'GGCC' 'GTTT' 'GCTC'\r\n 'GTTC' 'AAAA' 'CGGA' 'GATT' 'GTGG'\r\n 'TTAC' 'GGCG' 'GAGA' 'GGGG' 'TTGC'};\r\nassert(isequal(sequences, decode_genome(genome)));\r\n\r\n%%\r\ngenome = [1 4 16 64; 234 186 174 171];\r\nsequences = {'AAAC' 'AACA' 'ACAA' 'CAAA'; 'GTTT' 'TGTT' 'TTGT' 'TTTG'};\r\nassert(isequal(sequences, decode_genome(genome)));\r\n\r\n%%\r\ngenome = [228 225 216 210 198 201 180 177 156 147 135 141 108 99 120 114 78 75 39 45 27 30 54 57]';\r\nsequences = {'GTCA' 'GTAC' 'GCTA' 'GCAT' 'GACT' 'GATC' 'TGCA' 'TGAC' 'TCGA' 'TCAG' 'TACG' 'TAGC' 'CTGA' 'CTAG' 'CGTA' 'CGAT' 'CAGT' 'CATG' 'ATCG' 'ATGC' 'ACTG' 'ACGT' 'AGCT' 'AGTC'}';\r\nassert(isequal(sequences, decode_genome(genome)));","published":true,"deleted":false,"likes_count":2,"comments_count":0,"created_by":999,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":68,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":32,"created_at":"2014-08-17T10:20:31.000Z","updated_at":"2026-03-19T20:07:27.000Z","published_at":"2014-08-17T10:20:31.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eInspired by a question on the answer forum:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eYou are given a matrix of 8-bit integers which encodes a genome. Each integer can be converted into a sequence by converting it first to binary and then converting bit pairs using the rule A = 00, C = 01, T = 10, G = 11. For example, 177 -\u0026gt; 10110001 -\u0026gt; TGAC.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eConvert the matrix into a cell array of sequences.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003estr2num and regexp not allowed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":912,"title":"Genome Sequence 002: Introductory DNA Sequencing (Flipped Segments)","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssTACAGGTACCGGssss Middle\r\nsssssGGCCATGGACATssss Middle Reversed\r\nssssssssssssGACATTACG\r\nGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\r\nSegments may be flipped (Genome_002 change)\r\nLength of each segment - 48\r\nSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\nAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order will be scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\r\nExample: [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\r\nFuture: Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 727.2px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.6px; transform-origin: 407px 363.6px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 367px 8px; transform-origin: 367px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssTACAGGTACCGGssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 148px 8.5px; transform-origin: 148px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003esssssGGCCATGGACATssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 60px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 60px 8.5px; \"\u003eMiddle Reversed\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 384px 8px; transform-origin: 384px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 155px 8px; transform-origin: 155px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be flipped (Genome_002 change)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 241px 8px; transform-origin: 241px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 324px 8px; transform-origin: 324px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order will be scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 184px 8px; transform-origin: 184px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 317px 8px; transform-origin: 317px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n G=[];\r\nend","test_suite":"%%\r\ntic\r\nL=4176; % 1040 Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n% Flip random segments\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":5,"test_suite_updated_at":"2021-07-16T14:47:06.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-08-15T19:14:39.000Z","updated_at":"2021-07-16T14:47:06.000Z","published_at":"2012-10-01T03:42:15.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,TACAGGTACCGG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being flipped left-right.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssTACAGGTACCGGssss Middle\\nsssssGGCCATGGACATssss Middle Reversed\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_002 Challenge is to reconstruct a genome under near ideal segment creation conditions. Some of the segments will be reversed. The output may be reversed.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be flipped (Genome_002 change)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome or fliplr(Genome) vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 1 3 2 2; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2; Middle segment was flipped\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":863,"title":"Genome Sequence 001: Introductory DNA Sequencing","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. \u003chttp://en.wikipedia.org/wiki/Genome DNA Sequencing\u003e and the \u003chttp://en.wikipedia.org/wiki/Shotgun_sequencing Shot Gun Method\u003e will be naively simplified into Cody Challenges. \u003chttp://en.wikipedia.org/wiki/Genome_sequence Genome sizes\u003e is another interesting wiki page.\r\n\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches. \r\n\r\n*Example:* G = ACGTCGGCCATGGACATTACG\r\n\r\nGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\r\n\r\n ACGTCGGCCATGGACATTACG\r\n ACGTCGGCCAsssssssssss\r\n sssssGGCCATGGACATssss\r\n ssssssssssssGACATTACG\r\n\r\n\r\n\r\nGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\r\n\r\n# Length of each segment - 48\r\n# Segments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\r\n# All segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\r\n# Segments read left to right (no flips)\r\n# No errors in the segments\r\n# Genome is random (No duplicate starts or ends for 16 symbols of segments)\r\n# Segments will be scrambled\r\n\r\n*Input:* segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\n\r\n*Output:* Gout, Genome vector of values [0,1,2,3]\r\n\r\n*Example:* [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\r\n\r\n*Future:* Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)","description_html":"\u003cp\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing. \u003ca href=\"http://en.wikipedia.org/wiki/Genome\"\u003eDNA Sequencing\u003c/a\u003e and the \u003ca href=\"http://en.wikipedia.org/wiki/Shotgun_sequencing\"\u003eShot Gun Method\u003c/a\u003e will be naively simplified into Cody Challenges. \u003ca href=\"http://en.wikipedia.org/wiki/Genome_sequence\"\u003eGenome sizes\u003c/a\u003e is another interesting wiki page.\u003c/p\u003e\u003cp\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e G = ACGTCGGCCATGGACATTACG\u003c/p\u003e\u003cp\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003eACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nsssssGGCCATGGACATssss\r\nssssssssssssGACATTACG\r\n\u003c/pre\u003e\u003cp\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/p\u003e\u003col\u003e\u003cli\u003eLength of each segment - 48\u003c/li\u003e\u003cli\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/li\u003e\u003cli\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/li\u003e\u003cli\u003eSegments read left to right (no flips)\u003c/li\u003e\u003cli\u003eNo errors in the segments\u003c/li\u003e\u003cli\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/li\u003e\u003cli\u003eSegments will be scrambled\u003c/li\u003e\u003c/ol\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e Gout, Genome vector of values [0,1,2,3]\u003c/p\u003e\u003cp\u003e\u003cb\u003eExample:\u003c/b\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/p\u003e\u003cp\u003e\u003cb\u003eFuture:\u003c/b\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/p\u003e","function_template":"function Gout = Genome_001(segs)\r\n% s is an array of N segments of length 48\r\n G=[];\r\nend","test_suite":"tic\r\nL=4176; % 1040 Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n%%\r\ntic\r\nL=1040; % Special Selection for W=48 and 16 overlap\r\nGtruth=randi(4,1,L,'uint8')-1;\r\nsegs=zeros(floor(L/32),48);\r\nfor i=0:size(segs,1)-1 % Ideal Overlap segment creator\r\n segs(i+1,:)=Gtruth(i*32+1:i*32+48);\r\nend\r\nv=randperm(size(segs,1));\r\nsegs(:,:)=segs(v,:);\r\n\r\nGout = Genome_001(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth))\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":6,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":7,"test_suite_updated_at":null,"rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-24T19:18:06.000Z","updated_at":"2012-10-01T00:04:58.000Z","published_at":"2012-10-01T00:04:58.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Shotgun_sequencing\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://en.wikipedia.org/wiki/Genome_sequence\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping and duplicative segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e G = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GGCCATGGACAT, and GACATTACG these can be readily seen to overlap and create the original.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nsssssGGCCATGGACATssss\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_001 Challenge is to reconstruct a genome under ideal segment creation conditions.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments begin at locations 1, 33, 65,...32N+1 (N=0:K, L_Genome=32K+48)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments are provided once (Essentially two copies of a genome were cut into pieces with overlaps)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments read left to right (no flips)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments will be scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 2; 2 2 3 1; 3 1 1 2] creates [0 1 2 2 3 1 1 2] M=3,W=4, Overlap=2\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments, Random Position of Segment start locations, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments (Matlab - 19.2 sec single thread benchmark)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray type=\\\"array\\\"/\u003e\u003c/embeddedOutputs\u003e\"}]}"},{"id":797,"title":"Genome Sequence 003R: Sequence DNA of random positioned and flipped segments","description":"This is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments. DNA Sequencing is naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssGCCATGGACATCsssss Middle Rev\r\nssssCTACAGGTACCGsssss Middle flipped\r\nssssssssssssGACATTACG\r\nGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\r\nSegments may be reversed (Change from 003)\r\nSegments start at random positions\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 726.633px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 363.317px; transform-origin: 407px 363.317px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 341px 8px; transform-origin: 341px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 133.5px 8px; transform-origin: 133.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 368.5px 8px; transform-origin: 368.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 102.167px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 51.0833px; transform-origin: 404px 51.0833px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 128px 8.5px; transform-origin: 128px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssGCCATGGACATCsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 40px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 40px 8.5px; \"\u003eMiddle Rev\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 144px 8.5px; transform-origin: 144px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 56px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 56px 8.5px; \"\u003eMiddle flipped\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 382px 8px; transform-origin: 382px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 163.467px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 81.7333px; transform-origin: 391px 81.7333px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 148.5px 8px; transform-origin: 148.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments may be reversed (Change from 003)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 111.5px 8px; transform-origin: 111.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 324.5px 8px; transform-origin: 324.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 84px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 42px; text-align: left; transform-origin: 384px 42px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 355.5px 8px; transform-origin: 355.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003R(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=563*17;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n GtruthR=fliplr(Gtruth);\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n Gseg(j+L-15,:)=GtruthR(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==(L-15)*2\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=1;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\nf=logical(randi(2,size(segs,1),1)-1);\r\nsegs_orig=segs;\r\n\r\nsegs(f,:)=fliplr(segs(f,:));\r\n\r\n\r\n\r\nGout = Genome_003R(segs);\r\ntoc\r\n\r\nassert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\n%assert( isequal(Gout,Gtruth) )\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":3,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2021-07-16T14:52:10.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-06-27T17:37:02.000Z","updated_at":"2021-07-16T14:52:10.000Z","published_at":"2012-10-07T22:51:12.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis is Challenge 003R in the series on Genome DNA Sequencing. Challenge 3R includes flipped segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA, GCCATGGACATC, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as being reversed with asymetric overlaps to its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssGCCATGGACATCsssss Middle Rev\\nssssCTACAGGTACCGsssss Middle flipped\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003R Challenge is to reconstruct a genome under near ideal error free segment creation conditions. Segments may be reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments may be reversed (Change from 003)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2;1 1 2 2 3 2 ; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies, Reverses may occur\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003),Random Segment Positions with Flips (003R), Parrot Sequence with Gen3 Long Segments, Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":969,"title":"Genome Sequence 003: DNA Sequence with random positioned segments","description":"This Challenge series will evolve the complexity of Genome DNA Sequencing. DNA Sequencing and the Shot Gun Method will be naively simplified into Cody Challenges. Genome sizes is another interesting wiki page.\r\nDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\r\nExample: Genome = ACGTCGGCCATGGACATTACG\r\nGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\r\nACGTCGGCCATGGACATTACG\r\nACGTCGGCCAsssssssssss\r\nssssCTACAGGTACCGsssss Middle\r\nssssssssssssGACATTACG\r\nGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\r\nSegments start at random positions (Genome_003 change from 001)\r\nGenome length is unconstrained\r\nLength of each segment - 48\r\nAll segments may overlap by 16 to 47 characters\r\nNo errors in the segments\r\nGenome is random (No duplicate starts or ends for 16 symbols of segments)\r\nSegment order is scrambled\r\nInput: segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\r\nOutput: Gout, Genome vector of values [0,1,2,3]\r\nExample: [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\r\nFuture: Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments","description_html":"\u003cdiv style = \"text-align: start; line-height: 20.4333px; min-height: 0px; white-space: normal; color: rgb(0, 0, 0); font-family: Menlo, Monaco, Consolas, monospace; font-style: normal; font-size: 14px; font-weight: 400; text-decoration: rgb(0, 0, 0); white-space: normal; \"\u003e\u003cdiv style=\"block-size: 706.767px; display: block; min-width: 0px; padding-block-start: 0px; padding-top: 0px; perspective-origin: 407px 353.383px; transform-origin: 407px 353.383px; vertical-align: baseline; \"\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 243px 8px; transform-origin: 243px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eDNA Sequencing\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e and the\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eShot Gun Method\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e will be naively simplified into Cody Challenges.\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 2px 8px; transform-origin: 2px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e \u003c/span\u003e\u003c/span\u003e\u003ca target='_blank' href = \"/#null\"\u003e\u003cspan style=\"\"\u003e\u003cspan style=\"\"\u003eGenome sizes\u003c/span\u003e\u003c/span\u003e\u003c/a\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 101.5px 8px; transform-origin: 101.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e is another interesting wiki page.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 105px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 52.5px; text-align: left; transform-origin: 384px 52.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 369px 8px; transform-origin: 369px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 139px 8px; transform-origin: 139px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 366.5px 8px; transform-origin: 366.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgb(247, 247, 247); block-size: 81.7333px; border-bottom-left-radius: 4px; border-bottom-right-radius: 4px; border-end-end-radius: 4px; border-end-start-radius: 4px; border-start-end-radius: 4px; border-start-start-radius: 4px; border-top-left-radius: 4px; border-top-right-radius: 4px; margin-block-end: 10px; margin-block-start: 10px; margin-bottom: 10px; margin-inline-end: 3px; margin-inline-start: 3px; margin-left: 3px; margin-right: 3px; margin-top: 10px; perspective-origin: 404px 40.8667px; transform-origin: 404px 40.8667px; margin-left: 3px; margin-top: 10px; margin-bottom: 10px; margin-right: 3px; \"\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCATGGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003eACGTCGGCCAsssssssssss\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 112px 8.5px; transform-origin: 112px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; perspective-origin: 88px 8.5px; transform-origin: 88px 8.5px; \"\u003essssCTACAGGTACCGsssss \u003c/span\u003e\u003cspan style=\"border-block-end-color: rgb(170, 4, 249); border-block-start-color: rgb(170, 4, 249); border-bottom-color: rgb(170, 4, 249); border-inline-end-color: rgb(170, 4, 249); border-inline-start-color: rgb(170, 4, 249); border-left-color: rgb(170, 4, 249); border-right-color: rgb(170, 4, 249); border-top-color: rgb(170, 4, 249); caret-color: rgb(170, 4, 249); color: rgb(170, 4, 249); column-rule-color: rgb(170, 4, 249); margin-inline-end: 0px; margin-right: 0px; outline-color: rgb(170, 4, 249); perspective-origin: 24px 8.5px; text-decoration: none; text-decoration-color: rgb(170, 4, 249); text-emphasis-color: rgb(170, 4, 249); transform-origin: 24px 8.5px; \"\u003eMiddle\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"background-color: rgba(0, 0, 0, 0); block-size: 20.4333px; border-bottom-left-radius: 0px; border-bottom-right-radius: 0px; border-end-end-radius: 0px; border-end-start-radius: 0px; border-inline-end-color: rgb(233, 233, 233); border-inline-end-style: solid; border-inline-end-width: 1px; border-inline-start-color: rgb(233, 233, 233); border-inline-start-style: solid; border-inline-start-width: 1px; border-left-color: rgb(233, 233, 233); border-left-style: solid; border-left-width: 1px; border-right-color: rgb(233, 233, 233); border-right-style: solid; border-right-width: 1px; border-start-end-radius: 0px; border-start-start-radius: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; min-block-size: 18px; min-height: 18px; padding-inline-start: 4px; padding-left: 4px; perspective-origin: 404px 10.2167px; transform-origin: 404px 10.2167px; white-space: nowrap; \"\u003e\u003cspan style=\"block-size: auto; border-inline-end-color: rgb(0, 0, 0); border-inline-end-style: none; border-inline-end-width: 0px; border-inline-start-color: rgb(0, 0, 0); border-inline-start-style: none; border-inline-start-width: 0px; border-left-color: rgb(0, 0, 0); border-left-style: none; border-left-width: 0px; border-right-color: rgb(0, 0, 0); border-right-style: none; border-right-width: 0px; display: inline; margin-inline-end: 45px; margin-right: 45px; min-block-size: 0px; min-height: 0px; padding-inline-start: 0px; padding-left: 0px; perspective-origin: 84px 8.5px; transform-origin: 84px 8.5px; unicode-bidi: normal; white-space: pre; margin-right: 45px; \"\u003e\u003cspan style=\"margin-inline-end: 0px; margin-right: 0px; \"\u003essssssssssssGACATTACG\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 42px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 10px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 10px; perspective-origin: 384px 21px; text-align: left; transform-origin: 384px 21px; white-space: pre-wrap; margin-left: 4px; margin-top: 10px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 354px 8px; transform-origin: 354px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003col style=\"block-size: 143.033px; counter-reset: list-item 0; font-family: Helvetica, Arial, sans-serif; list-style-type: decimal; margin-block-end: 20px; margin-block-start: 10px; margin-bottom: 20px; margin-top: 10px; perspective-origin: 391px 71.5167px; transform-origin: 391px 71.5167px; margin-top: 10px; margin-bottom: 20px; \"\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 217px 8px; transform-origin: 217px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegments start at random positions (Genome_003 change from 001)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 102.5px 8px; transform-origin: 102.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome length is unconstrained\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 91px 8px; transform-origin: 91px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eLength of each segment - 48\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 153.5px 8px; transform-origin: 153.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eAll segments may overlap by 16 to 47 characters\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 81.5px 8px; transform-origin: 81.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eNo errors in the segments\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 240px 8px; transform-origin: 240px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli style=\"block-size: 20.4333px; counter-reset: none; display: list-item; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-start: 56px; margin-left: 56px; margin-top: 0px; perspective-origin: 363px 10.2167px; text-align: left; transform-origin: 363px 10.2167px; white-space: pre-wrap; margin-left: 56px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-inline-start: 0px; margin-left: 0px; perspective-origin: 88.5px 8px; transform-origin: 88.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003eSegment order is scrambled\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 20px 8px; transform-origin: 20px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eInput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 213px 8px; transform-origin: 213px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 26px 8px; transform-origin: 26px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eOutput:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 128.5px 8px; transform-origin: 128.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Gout, Genome vector of values [0,1,2,3]\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 21px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 10.5px; text-align: left; transform-origin: 384px 10.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 31.5px 8px; transform-origin: 31.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eExample:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 250px 8px; transform-origin: 250px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003cdiv style=\"block-size: 63px; font-family: Helvetica, Arial, sans-serif; line-height: 21px; margin-block-end: 9px; margin-block-start: 2px; margin-bottom: 9px; margin-inline-end: 10px; margin-inline-start: 4px; margin-left: 4px; margin-right: 10px; margin-top: 2px; perspective-origin: 384px 31.5px; text-align: left; transform-origin: 384px 31.5px; white-space: pre-wrap; margin-left: 4px; margin-top: 2px; margin-bottom: 9px; margin-right: 10px; \"\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 25.5px 8px; transform-origin: 25.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"font-weight: 700; \"\u003eFuture:\u003c/span\u003e\u003c/span\u003e\u003cspan style=\"block-size: auto; display: inline; margin-block-end: 0px; margin-block-start: 0px; margin-bottom: 0px; margin-inline-end: 0px; margin-inline-start: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; perspective-origin: 345.5px 8px; transform-origin: 345.5px 8px; unicode-bidi: normal; \"\u003e\u003cspan style=\"\"\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/span\u003e\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e\u003c/div\u003e","function_template":"function Gout = Genome_003(segs)\r\n% segs is an array of N segments of length 48\r\n% Construct the unique Gout sequence\r\n% Guaranteed 16 long blocks are unique\r\n Gout=[];\r\nend","test_suite":"%%\r\ntic\r\nL=1024;\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=2000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n%%\r\ntic\r\nL=4000+randi(200);\r\nwhile 1 % Loop until create a Gtruth with no repeated 16 segments\r\n Gtruth=randi(4,1,L,'uint8')-1;\r\n \r\n Gseg=zeros(L-15,16,'uint8');\r\n for j=1:L-15\r\n Gseg(j,:)=Gtruth(j:j+15);\r\n end\r\n Gsegv=uint32(Gseg(:,1));\r\n for j=2:16\r\n Gsegv=4*Gsegv+uint32(Gseg(:,j));\r\n end\r\n if size(unique(Gsegv),1)==L-15\r\n break\r\n end\r\nend % while create valid Gtruth\r\n\r\nsegs=Gtruth(1:48); % First segment is a required\r\nsegs=[segs;Gtruth(L-47:end)]; % Last Segment is required\r\nptr=0;\r\nwhile 1\r\n ptr=ptr+randi(32);\r\n if ptr+48\u003eL,break;end\r\n segs=[segs;Gtruth(ptr:ptr+47)];\r\nend\r\n\r\nv=randperm(size(segs,1)); % Segs Scrambled Over Easy\r\nsegs(:,:)=segs(v,:);\r\n\r\n\r\n\r\nGout = Genome_003(segs);\r\ntoc\r\n\r\n%assert(isequal(Gout,Gtruth)||isequal(Gout,fliplr(Gtruth)))\r\nassert( isequal(Gout,Gtruth) )\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":1,"comments_count":1,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":3,"test_suite_updated_at":"2021-07-16T14:46:09.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-10-03T04:17:33.000Z","updated_at":"2025-05-05T20:24:45.000Z","published_at":"2012-10-03T04:47:11.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis Challenge series will evolve the complexity of Genome DNA Sequencing.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eDNA Sequencing\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e and the\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eShot Gun Method\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be naively simplified into Cody Challenges.\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eGenome sizes\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e is another interesting wiki page.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eDNA is represented by symbols ACGT, which for Matlab will be encoded as 0123. The basic goal is to reconstruct the original serial string of ACGT given multiple short segments. Segments are gleaned from multiple copies of the Virus/Bacteria/Chromosome thus there are overlapping, duplicative, and flipped segments. There are potential errors and duplicative stretches in the created segments. Chromosome 20 in its 59,187,298 base pairs has a segment of 820 that is repeated in at least two locations. The data being non-random largely increase lengths of duplicative stretches.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Genome = ACGTCGGCCATGGACATTACG\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGiven three overlapping pieces, ACGTCGGCCA,CTACAGGTACCG, and GACATTACG these can be readily seen to overlap and create the original if the middle is recognized as having asymetric overlaps with its adjacent segments.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[ACGTCGGCCATGGACATTACG\\nACGTCGGCCAsssssssssss\\nssssCTACAGGTACCGsssss Middle\\nssssssssssssGACATTACG]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome_003 Challenge is to reconstruct a genome under near ideal error free segment creation conditions. No segments are reversed. The segments start at random locations.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegments start at random positions (Genome_003 change from 001)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome length is unconstrained\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eLength of each segment - 48\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eAll segments may overlap by 16 to 47 characters\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eNo errors in the segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome is random (No duplicate starts or ends for 16 symbols of segments)\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"ListParagraph\\\"/\u003e\u003cw:numPr\u003e\u003cw:numId w:val=\\\"2\\\"/\u003e\u003c/w:numPr\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eSegment order is scrambled\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e segs, Array of M rows of 48 value segments. Values are [0, 1, 2, 3].\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Gout, Genome vector of values [0,1,2,3]\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eExample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e [0 1 2 3 2; 1 2 3 2 2; 2 2 1 1 2] creates [0 1 2 3 2 2 1 1 2] W=5, Overlap=varies\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003cw:jc w:val=\\\"left\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eFuture:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Flipped segments(002), Random Position of Segment start locations(003), Extra Segments, Phage Phi X174, Parallel Processing Simulation(Shot Gun Approach), Haemophilus Influenza, Sequence with Segment Errors, and Chromosome 20 with its 59M length using 100K 4K-segments\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\",\"relationship\":null}],\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"target\":\"/matlab/document.xml\",\"relationshipId\":\"rId1\"}]}"},{"id":811,"title":"Genome Sequence 004: Long 3rd Generation Segment Correction","description":"The Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by \u003chttp://www.pacificbiosciences.com/ PacBio\u003e. The \u003chttp://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar Assemblathon Genome Contest\u003e led the team of Phillippy, Koren and Jarvis to successfully \u003chttp://www.sciencedaily.com/releases/2012/07/120702210229.htm Sequence Parrot DNA\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\r\n\r\nThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u003c1% error rate. Jarvis and his team combined this data to achieve \u003c 0.1% error rate.\r\n\r\nGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\r\n\r\n*Input:* \r\n\r\nCall 1: empty array, segment Width, Flag=0\r\n\r\nCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\r\n\r\n*Output:* \r\n\r\nCall 1: empty vector, Number of Requested Vectors\r\n\r\nCall 2: Corrected DNA vector, Number of Requested Vectors\r\n\r\n*Score:* Number of N vectors used to produce correct vector for w=1024 case\r\n\r\nThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\r\n\r\nThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\r\n\r\nThe response to the second call is the fixed DNA sequence, vector of width w.\r\n\r\n*example:*\r\nFirst call return : N=3\r\n\r\n 01230123111122223333 Truth\r\n Input example\r\n 01232123112122221332 Injected errors\r\n 01130123111122123323\r\n 11230133121122223333\r\n\r\n Output: \r\n 01230123111122223333 Truth, hopefully\r\n\r\n\r\nThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned. \r\n\r\nThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\r\n\r\nFollow-Up Challenges: Sample Data from the PacBio site for \u003chttp://www.cbcb.umd.edu/software/PBcR/ Lambda Phage\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\r\n","description_html":"\u003cp\u003eThe Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by \u003ca href=\"http://www.pacificbiosciences.com/\"\u003ePacBio\u003c/a\u003e. The \u003ca href=\"http://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar\"\u003eAssemblathon Genome Contest\u003c/a\u003e led the team of Phillippy, Koren and Jarvis to successfully \u003ca href=\"http://www.sciencedaily.com/releases/2012/07/120702210229.htm\"\u003eSequence Parrot DNA\u003c/a\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\u003c/p\u003e\u003cp\u003eThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u0026lt;1% error rate. Jarvis and his team combined this data to achieve \u0026lt; 0.1% error rate.\u003c/p\u003e\u003cp\u003eGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\u003c/p\u003e\u003cp\u003e\u003cb\u003eInput:\u003c/b\u003e\u003c/p\u003e\u003cp\u003eCall 1: empty array, segment Width, Flag=0\u003c/p\u003e\u003cp\u003eCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\u003c/p\u003e\u003cp\u003e\u003cb\u003eOutput:\u003c/b\u003e\u003c/p\u003e\u003cp\u003eCall 1: empty vector, Number of Requested Vectors\u003c/p\u003e\u003cp\u003eCall 2: Corrected DNA vector, Number of Requested Vectors\u003c/p\u003e\u003cp\u003e\u003cb\u003eScore:\u003c/b\u003e Number of N vectors used to produce correct vector for w=1024 case\u003c/p\u003e\u003cp\u003eThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\u003c/p\u003e\u003cp\u003eThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\u003c/p\u003e\u003cp\u003eThe response to the second call is the fixed DNA sequence, vector of width w.\u003c/p\u003e\u003cp\u003e\u003cb\u003eexample:\u003c/b\u003e\r\nFirst call return : N=3\u003c/p\u003e\u003cpre class=\"language-matlab\"\u003e01230123111122223333 Truth\r\nInput example\r\n01232123112122221332 Injected errors\r\n01130123111122123323\r\n11230133121122223333\r\n\u003c/pre\u003e\u003cpre class=\"language-matlab\"\u003eOutput: \r\n01230123111122223333 Truth, hopefully\r\n\u003c/pre\u003e\u003cp\u003eThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned.\u003c/p\u003e\u003cp\u003eThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\u003c/p\u003e\u003cp\u003eFollow-Up Challenges: Sample Data from the PacBio site for \u003ca href=\"http://www.cbcb.umd.edu/software/PBcR/\"\u003eLambda Phage\u003c/a\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\u003c/p\u003e","function_template":"function [M_fix,N]=PacBio_fix(M,w,flag)\r\n% 1st Call\r\n% M is empty\r\n% w is width of segment\r\n% flag is 0\r\n% Ouput is N, the number of segments requested to fix the segment\r\n% 2nd Call\r\n% M is an Nxw array of values [0:3]\r\n\r\n M_fix=[];\r\n N=1; % needed for 2nd call with flag==1\r\n if flag==0 % Requested number of Segments\r\n N=1;\r\n return;\r\n end\r\n\r\nM_fix=M(1,:);\r\n\r\n\r\nend","test_suite":"%%\r\nfeval(@assignin,'caller','score',0);\r\n%%\r\nM=[];\r\nflag=0;\r\nw=100;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n%%\r\nM=[];\r\nflag=0;\r\nw=6144;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n\r\n%%\r\n% Size Performance is based on w=1024 case\r\nM=[];\r\nflag=0;\r\nw=1024;\r\n[M_fix,N]=PacBio_fix(M,w,flag);\r\n\r\nM_truth=randi(4,1,w,'uint8')-1;\r\nM=repmat(M_truth,N,1);\r\n\r\n% Apply 15% substitution error\r\nqerr=floor(.15*N*w);\r\nerrvec=randi(N*w,qerr,1);\r\nerrval=randi(4,qerr,1)-1;\r\n\r\nM(errvec)=errval;\r\n\r\nflag=1;\r\ntic\r\n[M_fix,not_N]=PacBio_fix(M,w,flag);\r\ntoc\r\n\r\nassert(isequal(M_fix,M_truth),sprintf('Error Count=%i',sum(M_fix~=M_truth)))\r\n\r\nfeval(@assignin,'caller','score',min(20,N));\r\n\r\n\r\n","published":true,"deleted":false,"likes_count":0,"comments_count":0,"created_by":3097,"edited_by":null,"edited_at":null,"deleted_by":null,"deleted_at":null,"solvers_count":2,"test_suite_updated_at":"2012-10-08T02:30:34.000Z","rescore_all_solutions":false,"group_id":1,"created_at":"2012-07-01T05:26:57.000Z","updated_at":"2012-10-08T02:40:09.000Z","published_at":"2012-10-08T02:29:50.000Z","restored_at":null,"restored_by":null,"spam":false,"simulink":false,"admin_reviewed":false,"description_opc":"{\"relationships\":[{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/document\",\"targetMode\":\"\",\"relationshipId\":\"rId1\",\"target\":\"/matlab/document.xml\"},{\"relationshipType\":\"http://schemas.mathworks.com/matlab/code/2013/relationships/output\",\"targetMode\":\"\",\"relationshipId\":\"rId2\",\"target\":\"/matlab/output.xml\"}],\"parts\":[{\"partUri\":\"/matlab/document.xml\",\"relationship\":[],\"contentType\":\"application/vnd.mathworks.matlab.code.document+xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\"?\u003e\\n\u003cw:document xmlns:w=\\\"http://schemas.openxmlformats.org/wordprocessingml/2006/main\\\"\u003e\u003cw:body\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe Melopsittacus undulates genome, Parrot Budgerigar, was successfully sequenced in July 2012 using long 3rd Gen sequences provided by\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.pacificbiosciences.com/\\\"\u003e\u003cw:r\u003e\u003cw:t\u003ePacBio\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e. The\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://assemblathon.org/a-parrot-a-fish-and-a-snake-walk-into-a-bar\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eAssemblathon Genome Contest\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e led the team of Phillippy, Koren and Jarvis to successfully\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.sciencedaily.com/releases/2012/07/120702210229.htm\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eSequence Parrot DNA\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e using the PacBio 3rd Generation data and Illumina 2nd Gen data.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe 3rd gen PacBio data is very long, 1K-20K, but has 15% error rate. The Illumina data is 100-500 long with \u0026lt;1% error rate. Jarvis and his team combined this data to achieve \u0026lt; 0.1% error rate.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eGenome Challenge 004 is the correction of simplified PacBio simulated reads with high error rate.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eInput:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 1: empty array, segment Width, Flag=0\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 2: N PacBio DNA vectors (N x width), Segment Width, Flag=1\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eOutput:\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 1: empty vector, Number of Requested Vectors\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eCall 2: Corrected DNA vector, Number of Requested Vectors\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eScore:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e Number of N vectors used to produce correct vector for w=1024 case\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe first call to the PacBio_fix routine returns the number of vectors requested to produce a final product. This may be a function of w.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe second call to PacBio_fix will have a DNA matix (N x width) and flag=1.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe response to the second call is the fixed DNA sequence, vector of width w.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:rPr\u003e\u003cw:b/\u003e\u003c/w:rPr\u003e\u003cw:t\u003eexample:\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e First call return : N=3\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"code\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003e\u003c![CDATA[01230123111122223333 Truth\\nInput example\\n01232123112122221332 Injected errors\\n01130123111122123323\\n11230133121122223333\\n\\nOutput: \\n01230123111122223333 Truth, hopefully]]\u003e\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThis data is simplified by only having simple substitutions and the data sets are provided pre-aligned.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eThe real PacBio data is quite a bit more complicated. Values may be added, deleted, substituted, and are of varying lengths. This causes alignment issues.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003cw:p\u003e\u003cw:pPr\u003e\u003cw:pStyle w:val=\\\"text\\\"/\u003e\u003c/w:pPr\u003e\u003cw:r\u003e\u003cw:t\u003eFollow-Up Challenges: Sample Data from the PacBio site for\u003c/w:t\u003e\u003c/w:r\u003e\u003cw:r\u003e\u003cw:t\u003e \u003c/w:t\u003e\u003c/w:r\u003e\u003cw:hyperlink w:docLocation=\\\"http://www.cbcb.umd.edu/software/PBcR/\\\"\u003e\u003cw:r\u003e\u003cw:t\u003eLambda Phage\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:hyperlink\u003e\u003cw:r\u003e\u003cw:t\u003e will be molded into various Challenges. Possible challenges are correcting individual long segments and assembling multiple long segments into the full Lambda Phage genome. The Parrot genome is too big for Cody to solve in 50 seconds.\u003c/w:t\u003e\u003c/w:r\u003e\u003c/w:p\u003e\u003c/w:body\u003e\u003c/w:document\u003e\"},{\"partUri\":\"/matlab/output.xml\",\"contentType\":\"text/xml\",\"content\":\"\u003c?xml version=\\\"1.0\\\" encoding=\\\"UTF-8\\\" standalone=\\\"no\\\" ?\u003e\u003cembeddedOutputs\u003e\u003cmetaData\u003e\u003cevaluationState\u003emanual\u003c/evaluationState\u003e\u003clayoutState\u003ecode\u003c/layoutState\u003e\u003coutputStatus\u003eready\u003c/outputStatus\u003e\u003c/metaData\u003e\u003coutputArray type=\\\"array\\\"/\u003e\u003cregionArray 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