[BioPython] Non blocking blast.

[Pieter Laeremans]

Frank Kauff <fkauff at duke.edu> writes:

>
> I've a little (crude) script ready that does that, blasting a fasta file
> of sequences using threads. It can be useful for blasting a 96 plate of
> sequences overnight.
> But be careful - as Jeff mentioned, blast is a shared resource:
> - for each additional request in the blast queue, you'll get a 60 (or
> so) seconds penalty from NCBI: 60s for the second, 120s for the third,
> etc. Makes to many threads quite unattractive...
> - If you start too many blasts in a short time, after hitting some limit
> the only response will be a nice page saying 'Access denied due to
> possible misuse', and your IP will be blocked from further access to
> ncbi blast... You'll then have to write them a nice email and beg for
> grace. Happend to me while testing some automated blast feature :-) But
> the limit seems to be several 100 requests in like 24h, which is quite a
> lot.
>
> If you're interested in the script, send me an email.
>
> Frank


Thank you all very much for the input.  But I think I have no other
option than submitting one job at a time. Since it is of utmost
importance that I do not get blocked.

kind regards,

Pieter