[BiO BB] SWDA

[Diego Martinez]

thanks Ryan,
I will give it a shot.

Diego


--- Ryan Golhar <ryangolhar at hotmail.com> wrote:

> I did a java implementation of Smith-Waterman long ago and it was
> incorporated into Jaligner.  The source code is available at
> http://sourceforge.net/projects/jaligner.  The code has been reworked --
> looks much more complicated than what I initially wrote.    That should
> get you started.  As for speed, it wasn't slow, it worked very well...
> 
> 
> -----
> Ryan Golhar
> Computational Biologist
> The Informatics Institute at
> The University of Medicine & Dentistry of NJ
> 
> Phone: 973-972-5034
> Fax: 973-972-7412
> Email: golharam at umdnj.edu
> 
> -----Original Message-----
> From: bio_bulletin_board-admin at bioinformatics.org
> [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Diego
> Martinez
> Sent: Friday, September 17, 2004 2:42 PM
> To: bio_bulletin_board at bioinformatics.org
> Subject: Re: [BiO BB] SWDA
> 
> 
> I dont think it would be so slow on a couple of
> sequences, I just dont know how to do 
> recursion.I mean, SW is already like 
> 50 X slower than a banded implementation.
> 
> Diego
> 
> 
> --- Dan Bolser <dmb at mrc-dunn.cam.ac.uk> wrote:
> 
> > On Fri, 17 Sep 2004, Martin Gollery wrote:
> > 
> > >Yes, but it would be painfully slow!
> > >Marty
> > 
> > Even over two sequences?
> > 
> > 
> > 
> > 
> > >
> > >Dan Bolser wrote:
> > >
> > >> 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 
> > >> bioinformatics.
> > >> 
> > >> 
> > >> 
> > >>>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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> > >>>
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