Limiting the alignment length when using localalign

Hey guys! I'm trying to use 'localalign' to align two bacterial genomes and find all common hits between them. The problem is that I need to limit each hit to 20 bp or less which is why I'm not using 'nwalign' or 'multialign'. Does anyone have any recommendations on how to limit the size of the output instead of having the function return several hundred basepair alignments? Thank you in advance.

Answer 1

[Shresth Sharma]

Hi,

It is my understanding that you are trying to use ‘localalign’ function to align two different data sets and you are having difficulty with the way the result is presented as you need some formatting to continue your work. The ’localalign’ function can still be used with a property, so that the data is below a certain limit required as follows:

AlignStruct = localalign(Seq1, Seq2, ...'MinScore', MinScoreValue, ...) 
AlignStruct = localalign(Seq1, Seq2, ...'NumAln', NumAlnValue, ...) 

These commands will help you align your data accordingly as required. For more information on the ‘localalign’ you can go through the documentation link:

https://www.mathworks.com/help/bioinfo/ref/localalign.html

[Pallavi Bugga]

Hi Shresth,

Thanks for taking the time to reply to my question. I'm not sure how adjusting the 'MinScore' or 'NumAln' (number of aligned sequences) will help ensure that the sequences found by 'localalign' will be 20 bp or less. Often, sequences 100 bp or larger are being returned with many mismatched portions. Any feedback would be greatly appreciated.