[Biopython] BLAST against mouse genome only[MESSAGE NOT SCANNED]

[Peter]

On Fri, Jun 19, 2009 at 5:16 PM, Peter Saffrey <pzs at dcs.gla.ac.uk> wrote:
>
> Peter wrote:
>>
>> Can you tell us the sequence you are using, so we can try reproducing
>> the 404 error?
>
> It's attached.

Got it, thanks. I've just tied it at work about six times in a row with a few
variations to the options, and they all worked (taking a few minutes for
each search). Are you limiting the expectation threshold, or the number
of alignments/descriptions to return? With the default settings the page
returned is a BIG file which may explain a network problem... but a 404
error (page not found) is odd.

>> This *might* be related to a online BLAST issue Cymon recently
>> identified. I would try that fix, before bothering the NCBI about this:
>> http://lists.open-bio.org/pipermail/biopython-dev/2009-June/006216.html
>
> I've been having that problem too. I've installed his patch, but it hasn't fixed
> my 404 error.

OK, I have checked in the fix for the "\n\n" issue - I'm satisfied that it is
sensible even if I haven't verified it first hand.

>> I would also try doing this search manually via the website, you may get
>> a more helpful error - perhaps a CPU usage limit (long searches can
>> reach a time limit and get terminated).
>
> I don't get any problems with the web search. I'm using this page:
> http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=10090
> with the reference genome only.

The Biopython qblast function is calling http://blast.ncbi.nlm.nih.gov/Blast.cgi
internally, but that web interface doesn't allow us to pick these non-standard
databases, so a fair test (Biopython vs website) on the same URL isn't
possible. That's a shame.

Peter