[Biopython] Blast using Biopython

[Willis, Jordan R]

Tanya,

Does it have to be XML? Could you try -outfmt 7 and possibly request qseq and sseq which will return the aligned part of the sequence from the query and subject?

J
On Oct 15, 2013, at 9:40 AM, Tanya Golubchik <golubchi at stats.ox.ac.uk> wrote:

> Hi guys,
> 
> This is strictly speaking more about blast than biopython, but I was wondering if anyone has any tips on doing the following: searching for a hit in a nucleotide database using tblastn, but reporting the actual DNA sequence of the subject, rather than the translated protein sequence. Is there by any chance a way of extracting this from the XML output?
> 
> What I'm finding is that blastn sometimes misses the edges, where substitutions close the ends of my hit result in a truncated hit (rather than a complete hit with a mismatch or two). The full hit is reported correctly by tblastn, but of course this returns the protein translation rather than the original nucleotide sequence. It's probably a long shot, but just wondering if anyone has ideas -- the brute force approach would be to get the start and stop positions from tblastn and then extract and re-align this fragment to my query, but that seems redundant given that blast has already done this for me...
> 
> Thanks
> Tanya
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