[Biopython] BLAST against mouse genome only

[C. G.]

--- On Fri, 6/5/09, Peter Saffrey <pzs at dcs.gla.ac.uk> wrote:

> From: Peter Saffrey <pzs at dcs.gla.ac.uk>
> Subject: [Biopython] BLAST against mouse genome only
> To: biopython at lists.open-bio.org
> Date: Friday, June 5, 2009, 10:27 AM
> I'm sorry if this question is
> answered elsewhere.
> 
> I'd like to use the web-service BLAST through biopython to
> blast nucleotide sequences against the mouse genome with
> something like this (from the biopython recipes page):
> 
> >>> from Bio.Blast import NCBIWWW
> >>> fasta_string = open("m_cold.fasta").read()
> >>> result_handle = NCBIWWW.qblast("blastn", "nr",
> fasta_string)

I believe you only need to add an Entrez query parameter to the qblast like:

result_handle = NCBIWWW.qblast("blastn", "nr", entrez_query="mouse[orgn]", fasta_string)

Maybe the query would need to be adjusted to suited anything more specific you wanted but I have not used this through qblast myself just through the NCBI web interface.

-steve