[Biopython] BLAST against mouse genome only

Peter Saffrey pzs at dcs.gla.ac.uk
Fri Jun 5 16:27:25 UTC 2009


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)

This obviously blasts against all the non-redundant sequences. I'm only 
interested in mouse - how do I make my query more specific? I can't seem 
to find an option on this page:

http://www.ncbi.nlm.nih.gov/blast/blast_databases.shtml

Peter




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