Dan Bolser dmb at mrc-dunn.cam.ac.uk
Fri Sep 17 13:19:17 EDT 2004

On Fri, 17 Sep 2004, Martin Gollery wrote:

>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!

Can it be done in perl?

I think such an implementation could be very usefull for teaching

>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

More information about the BBB mailing list