[BiO BB] SWDA
Ryan Golhar
ryangolhar at hotmail.com
Fri Sep 17 15:01:52 EDT 2004
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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>
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