[Biopython] BLAST against mouse genome only
Peter Saffrey
pzs at dcs.gla.ac.uk
Fri Jun 5 12:27:25 EDT 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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