[BiO BB] Smith-Waterman on FPGA

Martin Gollery marty.gollery at gmail.com
Tue Oct 17 08:57:49 EDT 2006

Quite a few people have done this, Deepan. It is much easier than BLAST!
Compugen, TimeLogic, Progeniq, CLCbiosystems, Adaptive Genomics, Mitrion,
and several academic groups have ported it.


On 10/16/06, Deepan Chakravarthy <codeshepherd at gmail.com> wrote:
> Hello,
> I am curious to know if anyone has programmed Smith-Waterman algorithm
> into FPGA. I guess FPGA is being used to run BLAST. Anyone who is
> currently playing with FPGA and any of the sequence alignment
> algorithms please share your experience.
> Thanks
> Deepan Chakravarthy N
> http://www.codeshepherd.com
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Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
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