BioPython submit multiple online blasts

Question

Is it possible to submit multiple sequences to the Bio.Blast.NCBIWWW module at the same time? I've tried to create a function that runs my blast and have several of them run using multiprocessing, but I think the NCBI server boots me after a while and the connection stops working.

Answer 1

Here they detail how to properly use it:

http://www.ncbi.nlm.nih.gov/BLAST/Doc/node60.html

• Do not launch more than 50 threads.
• Wait for the RID of a BLAST before starting the next one.

Flooding the server can lead to many problems and eventually we may be forced to block access from sites which flood the severs with no warning. We strongly suggest you limit your scripts to not send a request until you receive a RID from the server. Alternatively please introduce a "sleep" command in your script which sends request no less then one once per three seconds.

Biopython does the wait for the RID for you, but if you launch several queries you are certainly going to be banned.

Answer 2

I don't know what sort of limits NCBI has on their service, but you may want to look into installing BLAST locally and running your queries that way. Biopython has support for local BLAST: http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec96