[BioPython] NCBIWWW.qblast with refseq by organism

[Michiel Jan Laurens de Hoon]

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