[Biopython] BLAST against mouse genome only
Peter Saffrey
pzs at dcs.gla.ac.uk
Fri Jun 19 07:22:52 EDT 2009
Peter wrote:
> You should be able to use entrez_query="txid10090[orgn]" instead of
> entrez_query="mouse[orgn]" if you want to use an NCBI taxon id. This
> syntax works in an Entrez search (and therefore in Bio.Entrez of course),
> and I would expect it to do the same in BLAST.
>
That does select the taxid, but this has the same effect as using
entrez_query="mouse[orgn]" - I get all mouse matches, when I only want
the reference sequence.
I think the right solution is to select the right database -
"gpipe/10090/ref_contig". This works with the BioPerl example found here:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
With biopython, it sometimes works but other times I get the urllib 404
error. It's less reliable with long sequences, so I wonder whether this
could be qblast not waiting long enough for the query results. Is this
possible? The Perl script linked above has a wait cycle in it.
Peter
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