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!


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
> __________________________________
> Do you Yahoo!?
> Yahoo! Mail - 50x more storage than other providers!
> http://promotions.yahoo.com/new_mail
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
Marty's Law- the number of Bioinformatics acronyms will double every 18 

More information about the BBB mailing list