[Biopython] BLAST against mouse genome only

[Peter Saffrey]

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