[BioPython] Smith-Waterman, anyone?

[Ewan Birney]

On Tue, 1 May 2001, Iddo Friedberg wrote:

> 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.

For proteins, psw as part of Wise2 will do a fine job (distribution at
ftp://ftp.sanger.ac.uk/pub/birney/wise2/ ) - make sure you give it enough
memory 

--- hmmm --- you don't seem to be able to change the amount of memory on
the command line. That's a bug. You can fix it in dynlibsrc/basematrix.h


(code snippet below. Pretty obvious what it is doing)


/* 20 MB assummed. Could break something? */
#define COMPILE_BASEMATRIX_MAX_KB 20000


speed for explicit memory is v. close to "ideal". Speed for linear space
memory is about 4* too slow from ideal.



> 
> 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/
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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