[Biopython] BLAST against mouse genome only

[Chris Fields]

On Jun 5, 2009, at 12:00 PM, C. G. wrote:

> --- 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

The other option is to change the remote database requested (if  
possible); this can be done for quite a few databases.  Here's the link:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html

chris