[BioPython] Parsing BLAST for ClustalW

Alex Garbino agarbino at gmail.com
Thu Aug 21 05:44:27 UTC 2008


Hello,

I'm a new python and biophython user.
I'm trying to pull a BLAST result, parse it into a csv with the
following fields:
protein name, organism, common name, protein length, and FASTA sequence
The goal is to then feed the fasta sequences into ClustalW (to do a
phylogeny tree, look for conserved regions, etc).

I've managed to do the blast search, and parse the results into xml
from python. However, I'm not sure how to grab the above information
and put it together, so that I can save a csv and push it into
clustalw.

Could someone help?

Thanks!
Alex



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