[BioPython] NCBIWWW.qblast with refseq by organism
Michiel Jan Laurens de Hoon
mdehoon at c2b2.columbia.edu
Fri Jun 2 00:57:35 UTC 2006
Denil Wickrama wrote:
> Hi, I would like to BLAST a list of proteins against the refseq
> database and retrieve the corresponding accession numbers of the
> exact hits. I get errors when I change from the nr database to the
> refseq database. Also I am trying to restrict the results by organism
> name, but that was not successful.
> result_handle = NCBIWWW.qblast("blastp", "nr", seq,
entrez_query='"rattus norvegicus"
> [Organism]')
> result_handle = NCBIWWW.qblast("blastp", "refseq", seq,
entrez_query='"rattus norvegicus" [Organism]')
> Is it possible to do refseq searches with NCBIWWW.qblast?
It turns out that the NCBI server actually wants "refseq_protein"
instead of "refseq". (You can check this by saving NCBI's
Protein-protein blast page in HTML, and looking at the source). So if
you replace "refseq" by "refseq_protein", your code should run.
Restricting the results by organism worked fine for me with the
entrez_query you have.
--Michiel.
--
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032
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