[BiO BB] SWDA

[Dan Bolser]

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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>
>