[BioPython] pairwise alignment

[Jeffrey Chang]

Yes, pairwise2 can handle this.  You can pass in dictionary whose keys
are tuples of letters, e.g. ("V", "I"), and returns its match score.
The module is actually very flexible in terms of what kinds of
parameters it accepts for the match scores and gap penalties.  The
documentation could probably be clearer, though...

Jeff



On Thu, Oct 31, 2002 at 02:00:51PM -0800, Iddo Friedberg wrote:
> Hi,
> 
> Do we have a pairwise alignment module which can use scoring matrices? I 
> only know of Bio.pairwise2 which uses a match/mismatch scoring scheme.
> 
> Thanks,
> 
> Iddo
> 
> -- 
> Iddo Friedberg
> The Burnham Institute
> 10901 N. Torrey Pines Rd.
> La Jolla, CA 92037
> USA
> Tel: +1 (858) 646 3100 x3516
> Fax: +1 (858) 646 3171
> 
> 
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