[BioPython] Remote PSI-Blast

Raul Guerra colochera at gmail.com
Tue May 20 12:08:22 EDT 2008


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


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