[Biopython] BLAST against mouse genome only

[Peter]

On Fri, Jun 19, 2009 at 4:16 PM, Peter Saffrey<pzs at dcs.gla.ac.uk> wrote:
> Peter wrote:
>>
>> Maybe you caught the NCBI during a busy period?
>>
>
> I've been trying it throughout today and it works about 10% of the time.
> This is on a long sequence - 7kb; it always works on the 3kb examples I
> need and shorter. It also works fine when querying the 7kb against the ecoli
> database.
>
> Still, it sounds like the 404 problems may not be down to biopython. Do you
> think it's worth contacting NCBI directly?

Can you tell us the sequence you are using, so we can try reproducing
the 404 error?

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 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).

Peter