[BioPython] Remote PSI-Blast

[Raul Guerra]

Hello Everybody,

I just began using Biopython.I need to do a remote PSI-Blast, and I cannot
find how to do it online.

Does anybody know how to do it? Is it implemented in BioPython or do I have
to implement it?

Also,
I am trying to do a blastp for a fasta file named fastaStr, but I want to
restrict the sarch to the organim Chlamydomonas. Everytime I run the
following code

result_handle = NCBIWWW.qblast("blastp", "nr", fastaStr,
entrez_query='"Chlamydomonas" [ORGN]')

I get

 urllib2.URLError: <urlopen error (110, 'Connection timed out')>

from the Biopresult_handle = NCBIWWW.qblast("blastp", "nr", fastaStr,
entrez_query='"Chlamydomonas" [ORGN]')

from the Biopython code. Any ideas?


Thank you in advance,

David Guerra
Colgate University '09