[Biopython] BLAST against mouse genome only
C. G.
cg5x6 at yahoo.com
Fri Jun 5 13:00:29 EDT 2009
--- 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
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