Martin Gollery mgollery at unr.edu
Fri Sep 17 13:31:12 EDT 2004

Yes, but it would be painfully slow!

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.
>>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
>>>Do you Yahoo!?
>>>Yahoo! Mail - 50x more storage than other providers!
>>>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
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Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
Marty's Law- the number of Bioinformatics acronyms will double every 18 

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