Limiting the alignment length when using localalign
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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.
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Shresth Sharma
2020-3-20
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:
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