[Biopython] BLAST against mouse genome only

[Peter Saffrey]

(trying to reply to a digest - apologies if this ends up in the wrong place)

Thanks for the help - I'm still not quite there with this. The first suggestion was to add and entrez_query="mouse[orgn]" argument. This works, but it gives me everything in the mouse database - bacterial clones and all sorts. I just want the matches against the reference sequence. Can I tune this further?

The second suggestion was to use a database from the list here:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html

I've tried doing a query like this:

result_handle = NCBIWWW.qblast("blastn", "gpipe/10090/ref_contig", seq)

and it gives me urllib2.HTTPError 404s. I've also tried the database as "10090/refcontig" and using "refcontig" as the database with the entrez_query - they give blank results or internal server errors.

Using the cgi page here:

http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=10090

And selecting the reference genome gives me exactly the results I want; I can even spit out a URL for those options. However, I can't figure out how to set the taxid for a biopython query. Any ideas?

Sorry to be so verbose. I thought blasting against the reference genome ought to be pretty straight forward, but I seem to be struggling a bit...

Peter