[Biopython] qblast against RefSeq

[David Winter]

Hi Miguel, 

I think you want 'refseq_protein' (check out the drop-down on the web blast page, which shows you the available databases). 

The xml file returned by qblast will probably have a useful error message too. 

Cheers,
David


________________________________________
From: biopython-bounces at lists.open-bio.org [biopython-bounces at lists.open-bio.org] on behalf of Miguel Romero [phyrexian.kavu at gmail.com]
Sent: Sunday, 9 December 2012 4:53 p.m.
To: biopython at lists.open-bio.org
Subject: [Biopython] qblast against RefSeq

Hi!
Im learning how to run BLAST over the internet and Im interested in
blasting against the RefSeq database. For now I have managed to blast
against the nr database with:

result_handle = NCBIWWW.qblast("blastp", "nr", sequence_string)

but I dont know how to search against RefSeq, if I enter:

result_handle = NCBIWWW.qblast("blastp", "refseq", sequence_string)

the blast record is empty! Is it possible to blast against the RefSeq
database? What should I type in the second argument?

Thank you!

Miguel Romero

--
[Theropoda is my profession]
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