[Biopython] query upper limit for NCBIWWW.qblast?

[Peter Cock]

Dan replied via the digest (summary emails rather than individual emails) here:
http://lists.open-bio.org/pipermail/biopython/2013-April/008507.html

On Thu, Apr 11, 2013 at 9:51 PM, Dan <dan837446 at gmail.com> wrote:
> This is peripherally relevant to the question, I asked Tao Tao of NCBI user
> services about general guidelines for remote blast, and got this response:
>
> "In general, the key is to reduce the hits to BLAST server:
> At the search step, DO NOT submit searches that contain only single
> sequence! You need to batch the query and submit a set in a single search
> request.
> At the result polling step, you should reduce the result checking by
> spacing them out, and start checking for results after a delay (a few
> minutes).
> The XML result for batch queries is a bit peculiar each query is wrapped
> around  <Iteration> tag
> You are better off leaving the other conditions default and post-process it
> to get the top hits"
>
> Also it's best to search between 9PM and 5AM Eastern Standard time and at
> weekends.
> Personally I seem to encounter glitches using batches above 100 but it's so
> specific to your particular workplace that I'm not sure if that's a good
> guideline.
>

Perhaps Biopython's QBLAST wrapper could benefit from adaptive
time delays in the polling step - at the moment it just checks every
three seconds.

Peter