[BiO BB] SWDA

[Diego Martinez]

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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> 


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