[BiO BB] SWDA

Martin Gollery mgollery at unr.edu
Fri Sep 17 12:59:06 EDT 2004


Hi Diego,

I looked for this a couple of years ago whilst working on it for the 
DeCypher. There was nothing at the time, but this might have changed. I 
certainly like the double-affine scoring, so if there is no publicly 
available implementation, somebody ought to get to work on it!

Marty

Diego Martinez wrote:
> Hello all,
> 
> I am searching for an implementation of the Smith-Waterman
> algorythm, but with the double-affine gapping that is
> publicly available.  I know FASTA has a full SW implementation,
> but it does not offer the second gap penalty score option.
> I also am aware that Paracel and DeCypher both have these,
> but they are far from free.  Any help would be
> appreciated.
> 
> Thanks.
> 
> Diego
> 
> 
> 		
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-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
-----------
Marty's Law- the number of Bioinformatics acronyms will double every 18 
months.



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