[Biopython] qblast against RefSeq
David Winter
winda002 at student.otago.ac.nz
Sun Dec 9 05:06:48 UTC 2012
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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