[BiO BB] SWDA

[Ryan Golhar]

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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