[BioPython] Blast to genome specific databases?

[Chris Fields]

If you follow the directions on this page:

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

you should be able to modify the URLAPI DATABASE parameter to that in  
the list; another option would be to limit the results to a specific  
taxid (like 9606) using the ENTREZ_QUERY.  Not sure how that would be  
done for biopython (being a bioperler myself) but I'm sure someone  
could chip in?

chris

On Aug 20, 2007, at 12:48 PM, Emanuel Hey wrote:

> NCBI has a blast form for genome specific datbases
> that returns more information than does a blast to the
> generic nucleotide database
>
> http://www.ncbi.nlm.nih.gov/BLAST/
>
> See e.g. for the human genome
>
> http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi? 
> taxid=9606
>
>
> I've used NCBIWWW.qblast and used biopython for stand
> alone blasting,  but otherwise am not that experience.
>
>
> Is there a way to script a search that generates the
> same results as provided by these newere genome
> specific interfaces?
>
> Thanks
>
> Jhey
>
>
>
>
> ______________________________________________________________________ 
> ______________
> Got a little couch potato?
> Check out fun summer activities for kids.
> http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities 
> +for+kids&cs=bz
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign