[BioPython] public Smith-Waterman implementation?

[Iddo Friedberg]

Hi,

In Wise2 there is a protein Smith-Waterman implementation:

http://www.ebi.ac.uk/Wise2/doc_wise2.html#SECTION00082000000000000000

Also, you can try "water" from EMBOSS.

Biopython also has a Smith-Waterman code. Bio.pairwise2

Best,

Iddo


--- Joanne Adamkewicz <jadamkew at exelixis.com> wrote:

> Hi all,
> 
> A non-python related question, but very much in biocomputing:
> 
> Can someone point me to a publicly available implementation of the
> Smith-Waterman algorithm?  I'm aware of wise2
> (http://www.ebi.ac.uk/Wise2/doc_wise2.html), but it implements swp
> (protein-protein) only.  I'm looking for something that also
> includes tswn
> and the others.
> 
> Thanks in advance for any help,
> Joanne
> 
> _______________________________________________
> BioPython mailing list  -  BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 


=====
--
Iddo Friedberg                   
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA, 92037
USA 
T: (858) 646 3100 x3516
http://ffas.ljcrf.edu/~iddo


		
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