[BioPython] Smith-Waterman, anyone?

[Iddo Friedberg]

Hi,

Does anybody have a nice (preferably fast) program which implements the
Smith-Waterman local pairwise alignment algorithm? I'm looking for
something which accepts 2 strings (better yet: BioPython sequence objects)
and a substitution matrix as input, and gives some sort of intelligble
output.

Thanks,

Iddo

--

Iddo Friedberg                                  | Tel: +972-2-6758647
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg@cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/