[BiO BB] SWDA

[Diego Martinez]

Double Affine has two gap extension scores,
the second implemented after a specified
number of mismatches.  you get a longer, more
accurate alignment than BLASTP, I mean that as
it iddentifies more AA's in common.  I deal 
with very distant proteins most often.

Diego



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

> And why would you want to use a double-affine scoring scheme?  What
> benefits does it have?
> 
> Ryan
> 
> 
> 
> -----Original Message-----
> From: bio_bulletin_board-admin at bioinformatics.org
> [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Dan
> Bolser
> Sent: Friday, September 17, 2004 1:56 PM
> To: bio_bulletin_board at bioinformatics.org
> Subject: Re: [BiO BB] SWDA
> 
> 
> 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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