genbankread

Read data from GenBank file

Syntax

GenBankData = genbankread(File)

GenBankData = genbankread(File, TimeOut=TimeOutValue)

Description

GenBankData = genbankread(File) reads a GenBank-formatted file, File, and creates GenBankData, a structure or array of structures, with the fields corresponding to the GenBank^® keywords.

GenBankData = genbankread(File, TimeOut=TimeOutValue) sets the connection timeout (in seconds) to read data from a remote file or URL.

Examples

Data from GenBank File

Retrieve sequence information for the HEXA gene, store the data in a file, and then read into the MATLAB® software.

getgenbank("nm_000520",ToFile="TaySachs_Gene.txt")
s = genbankread("TaySachs_Gene.txt")

s = struct with fields:
                LocusName: 'NM_000520'
      LocusSequenceLength: '4785'
     LocusNumberofStrands: ''
            LocusTopology: 'linear'
        LocusMoleculeType: 'mRNA'
     LocusGenBankDivision: 'PRI'
    LocusModificationDate: '05-OCT-2024'
               Definition: 'Homo sapiens hexosaminidase subunit alpha (HEXA), transcript variant 2, mRNA.'
                Accession: 'NM_000520'
                  Version: 'NM_000520.6'
                       GI: ''
                  Project: []
                   DBLink: []
                 Keywords: 'RefSeq; MANE Select.'
                  Segment: []
                   Source: 'Homo sapiens (human)'
           SourceOrganism: [4×65 char]
                Reference: {[1×1 struct]  [1×1 struct]  [1×1 struct]  [1×1 struct]  [1×1 struct]  [1×1 struct]  [1×1 struct]  [1×1 struct]  [1×1 struct]  [1×1 struct]}
                  Comment: [46×66 char]
                 Features: [160×74 char]
                      CDS: [1×1 struct]
                 Sequence: 'ctcacgtggccagccccctccgagaggggagaccagcgggccatgacaagctccaggctttggttttcgctgctgctggcggcagcgttcgcaggacgggcgacggccctctggccctggcctcagaacttccaaacctccgaccagcgctacgtcctttacccgaacaactttcaattccagtacgatgtcagctcggccgcgcagcccggctgctcagtcctcgacgaggccttccagcgctatcgtgacctgcttttcggttccgggtcttggccccgtccttacctcacagggaaacggcatacactggagaagaatgtgttggttgtctctgtagtcacacctggatgtaaccagcttcctactttggagtcagtggagaattataccctgaccataaatgatgaccagtgtttactcctctctgagactgtctggggagctctccgaggtctggagacttttagccagcttgtttggaaatctgctgagggcacattctttatcaacaagactgagattgaggactttccccgctttcctcaccggggcttgctgttggatacatctcgccattacctgccactctctagcatcctggacactctggatgtcatggcgtacaataaattgaacgtgttccactggcatctggtagatgatccttccttcccatatgagagcttcacttttccagagctcatgagaaaggggtcctacaaccctgtcacccacatctacacagcacaggatgtgaaggaggtcattgaatacgcacggctccggggtatccgtgtgcttgcagagtttgacactcctggccacactttgtcctggggaccaggtatccctggattactgactccttgctactctgggtctgagccctctggcacctttggaccagtgaatcccagtctcaataatacctatgagttcatgagcacattcttcttagaagtcagctctgtcttcccagatttttatcttcatcttggaggagatgaggttgatttcacctgctggaagtccaacccagagatccaggactttatgaggaagaaaggcttcggtgaggacttcaagcagctggagtccttctacatccagacgctgctggacatcgtctcttcttatggcaagggctatgtggtgtggcaggaggtgtttgataataaagtaaagattcagccagacacaatcatacaggtgtggcgagaggatattccagtgaactatatgaaggagctggaactggtcaccaaggccggcttccgggcccttctctctgccccctggtacctgaaccgtatatcctatggccctgactggaaggatttctacatagtggaacccctggcatttgaaggtacccctgagcagaaggctctggtgattggtggagaggcttgtatgtggggagaatatgtggacaacacaaacctggtccccaggctctggcccagagcaggggctgttgccgaaaggctgtggagcaacaagttgacatctgacctgacatttgcctatgaacgtttgtcacacttccgctgtgaattgctgaggcgaggtgtccaggcccaacccctcaatgtaggcttctgtgagcaggagtttgaacagacctgagccccaggcaccgaggagggtgctggctgtaggtgaatggtagtggagccaggcttccactgcatcctggccaggggacggagccccttgccttcgtgccccttgcctgcgtgcccctgtgcttggagagaaaggggccggtgctggcgctcgcattcaataaagagtaatgtggcatttttctataataaacatggattacctgtgtttaaaaaaaaaagtgtgaatggcgttagggtaagggcacagccaggctggagtcagtgtctgcccctgaggtcttttaagttgagggctgggaatgaaacctatagcctttgtgctgttctgccttgcctgtgagctatgtcactcccctcccactcctgaccatattccagacacctgccctaatcctcagcctgctcacttcacttctgcattatatctccaaggcgttggtatatggaaaaagatgtaggggcttggaggtgttctggacagtggggagggctccagacccaacctggtcacagaagagcctctcccccatgcatactcatccacctccctcccctagagctattctcctttgggtttcttgctgcttcaattttatacaaccattatttaaatattattaaacacatattgttctctaggcactgtggtagtgggtttttttgttgtttttgtttttgagactgtctcaaaaactctgtcgcccaggctgacagtgcagtggcacaatcttggctcactgcagcctctgcctcctgggttcaagcgattctcgtgcatcagcctcctgagtaactggaattaataggcacgtgccaccatgtccatctaattcatatatatatattttttttttctgagacggagtctcactgtcacacaggctggagtgcagtggcacgatctcgactcactgcaagctccacctcctgggttcacgccattctcctgcctcagcctccccagtagctgggactacaggcgcccgccaccacgcccggctaattttttgtatttttagtagagatggggtttctccgtgttagccaggatggtctcgatctcctgacctcgtgatccgcccgccttggcctcccaaagtgctgggattacaggcgtgagccaccgcgcccggccgaattcatctatttttagtagagatggggtttcactatattggccaggctggtcttgaactcatgacctcagatgttcacttgtcttggcctcccaaagtgctgggattagaggcgtgagccaccgcacgcgggcctgtggtaaattgttgaatttgaaggactcagaggccctggtcaattccaaaataacgtaggcgacttccatccccctcctcccaaccattttcagcccaaagcatcttcgcagggaatggatggctgcgcggaggtgggcggtggctctggagagggtctttgcaggtgtgattttctctagaaggaaatgtctcgtcgtggacccagactgccccctcctggtttcagatgcagaagtgatactgtaagccagaggcgggggcagtaatgcatcgcagccattttaggtgaggatttccttggcggttatttgttaagttctttggctgggccctgggctggggtaacaatggacaggttccaggcatttttttcagaaagcttccagtgtagtggatacagaaacttcaggaaggcagggctgagaaggatctgagtaaaactcggtccttcaacaccatccttcagcccctgggtcatgttccttcgaggtcctggtgggaggtagacaagcctagccttgtgctgttcctgtaaggacagggtgggcattttctaccaacagaattcttggaattttcacacagcccagcctagccaagtccagggctatagcccagatacacaagttaaggtcccagcactggcacccaccacaggagcccccttacctctattacccagaagcttgtaggaggggtggtccgcagacaaggaccctgcacaggtgcgaccctgcttccctcctggtcataactttcatgttactattgcttgggataatgttaagtaaaaatagcagacactgagttttaagtctcaagtggatgaaggcagagatcgtgatacacttgagttaaagcagtagggttctgtcattttctattcctgttgtaaacattttctttaatgttattatttttaccactaaactaacgtggcctggtcacgactttcattggtaaagtgtgctgttcctcaccctccaccgttgctcctttggtccactgatcataagagcatttacctgaaggtcgtcagacctcgaatgccaacaggtcaactgcagtggcctgcagttaccacccagtctgttccaatgaacagaatcgctgttgccccaactcatctcccttcacctaggctgtaaattgaaagtcccacccctgagcggaacacaggccatcttgtgtgctgtgcaccaccagggggtggggaagtttccagactgacttcctggctccagtcatcctaggaaaagagttctccagtcgctccccacccccaccccttcccattccaggagtctattaaggaggcaaagcaggcctaacgggtatcaaagcaaaggagtgaatggagactgggagagtcttcaacctctcctctccttggtaggagctgaggctgcatgccaggtaccttcccttcgaggaatctaataaagctaggtcactggtgttttcaggtgcttctcaaaggattgccgtaggggtaggatatcaggatgtgggagcacaggtgccaccacagcactagtgatggagagtcattgcccctagacttctgggacagtgagactgtgaggaaagctgaaatgatactgggaaagggtgaaagaaaggatgtaggtggaatttatttagtattaatgtaggtacacataccttatggcaacattcctagcactctaaattctagatttgtatagtttctgtcaatatcttttgtaagcttaatcaatacagggcatgacaagtatgtgtcacatacttttttttccacgaagaaaaaaaataagtaggaattgggtgctttgtttatcaaaatttgtatttcctttataaataaactttgaaataaaggttgaaaattagta'

Display the source organism for this sequence.

s.SourceOrganism

ans = 4×65 char array
    'Homo sapiens                                                     '
    'Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;'
    'Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;     '
    'Catarrhini; Hominidae; Homo.                                     '

Input Arguments

File — GenBank-formatted file

string | character vector | string vector | character array

GenBank-formatted file, specified as one of these values:

• Character vector or string specifying a file name, a path and file name, or a URL pointing to a file. The referenced file is a GenBank-formatted file (ASCII text file). If you specify only a file name, that file must be on the MATLAB^® search path or in the MATLAB Current Folder.

• MATLAB character array or string vector that contains the text of a GenBank-formatted file.

You can use the getgenbank function with the ToFile argument to retrieve sequence information from the GenBank database and create an GenBank-formatted file.

Data Types: char | string

TimeOutValue — Connection timeout in seconds

5 (default) | positive number

Connection timeout in seconds, specified as a positive number. The default value is 5. For details, see here.

Data Types: double

Output Arguments

GenBankData — Resulting data

structure array

Resulting data, returned as a MATLAB structure or array of structures containing fields corresponding to GenBank keywords.

When File contains multiple entries, each entry is stored as a separate element in GenBankData. For a list of the GenBank keywords, see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html.

Version History

Introduced before R2006a