Get Snps, Indels From Biopython Blast Parser

Question

[Richard]

Hi all,

Is there a way through the bioPython API to get the list of variants from BLAST alignments?

I have done my alignments using standalone BLAST by providing -query and -subject, and the output is stored in an xml file that bioPython can parse. I am wondering if there are any provided methods that can report the snps, ins, del from within any hsp records.

If there are no methods can anyone provide an example of how to get snps, indels, dels in query 1-based coordinates. Ie. I guess you could get snvs from the "match" field, but how will insertions or deletions be represented?

thanks, RIchard

Answer 1

[Ryan Thompson]

I suppose you would have to look in the aligned portions of the query and subject for runs of dashes in order to find indels. Then you would have to count the number of non-gaps preceding the indel in the query and add that to the start position of the hsp.