[BioPython] Smith Waterman

[James Stroud]

Hello Everyone,

I am brand new to the biopython mailing list but I've been a python programmer 
for some time. Anyway, I have what I think is a naieve question, but I have 
tried to google this and I can't for the life of my find a complete answer 
anywhere. Basically, I want to do a Smith-Waterman with a Blosum matrix. I 
think I have the latest distro of biopython.

I have found the pairwise2 module and determined that I need:

 pairwise2.align.localdd()

But I'm not sure where the Blosum Matrix is in the biopython API. Any 
suggestions? A code snippet would be a lot of help.

James

-- 
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095

http://www.jamesstroud.com/