[Biopython] BLAST against mouse genome only

[Peter]

On Thu, Jun 18, 2009 at 6:51 PM, Peter Saffrey<pzs at dcs.gla.ac.uk> wrote:
>
> (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?
> ...
> Using the cgi page here:
>
> http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=10090
> ...
> However, I can't figure out how to set the taxid for a biopython query.
> Any ideas?

You should be able to use entrez_query="txid10090[orgn]" instead of
entrez_query="mouse[orgn]" if you want to use an NCBI taxon id. This
syntax works in an Entrez search (and therefore in Bio.Entrez of course),
and I would expect it to do the same in BLAST.

Peter