[BiO BB] SWDA

[Martin Gollery]

Yes, but it would be painfully slow!
Marty

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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-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
-----------
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months.