[BioPython] native python sequence alignment

[Frank Kauff]

Hi,

there's the pairwise2 module in biopython which is pretty
straightforward and does a nice job. Not excitingly fast, but if you
have short seqs anyway, it shouldn't matter.

Frank

On Wed, 2005-03-30 at 17:07 -0500, Syd Diamond wrote:
> Hi yall,
> 
> I need to do pairwise sequence alignment of short alphanumeric strings,
> and I turned to biopython to look for this tool.  I was hoping to do it
> natively and not need to repeatedly use a wrapper to ClustalW or something
> like that.  In scriptcentral, I found:
> 
> http://starship.python.net/crew/gherman/potpurri/align/

> 60% of the time, it works every time.  However, it's not quite perfect,
> and before I went diving into the heart of the alignment function, I
> wanted to see if anyone knew of a better approach or alternate code.  I've
> googled extensively without luck.
> 
> Many thanks,
> Joel
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-- 
Frank Kauff
Dept. of Biology
Duke University
Box 90338
Durham, NC 27708
USA

Phone 919-660-7382
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