[Biopython] How to restrict blast query to proteins of a certain species

[bar tomas]

Hi,
I just tried using a taxonomic id:
The following both give the same result:


result_handle = NCBIWWW.qblast(*"blastp"*, *"nr"*,
fasta_string,entrez_query=*"house mouse[orgn]"*)

result_handle = NCBIWWW.qblast(*"blastp"*, *"nr"*,
fasta_string,entrez_query=*"txid10090[orgn]"*)

(entrez_query needs to be after the non keyword arguments or else the
compiler complains)




On Fri, Aug 28, 2009 at 4:19 PM, Kelly F Oakeson <kelly.oakeson at utah.edu>wrote:

> Hell list,
> I would like to do something similar, but I would like to limit my
> blast search to just the microbial Taxonomic ID.
>
> Thanks,
>
> Kelly Oakeson
> kelly.oakeson at utah.edu
>
>
>
>
>  On Aug 28, 2009, at 8:17 AM, bar tomas wrote:
>
> > Hi,
> >
> > I'd like to use blast to measure homology  between protein sequences
> > of a
> > species and polyketide sequences from a database.
> > I've been looking in the Biopython tutorial(p.73) in the section about
> > blast.
> > I'd like to do something similar,  like this:
> >
> > result_handle = NCBIWWW.qblast("blastp", "genbank", record.format
> > ("fasta"))
> >
> > Is it possible to add an option to restrict the search to genbank
> > records
> > that correspond to a given species?
> >
> > Thanks very much
>  > _______________________________________________
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>
>