[BioPython] Blast to genome specific databases?
Chris Fields
cjfields at uiuc.edu
Mon Aug 20 15:17:48 EDT 2007
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
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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