[BiO BB] Smith-Waterman on FPGA

William Harman wharman at prism.net
Tue Oct 17 18:11:41 EDT 2006

The algorithm Starbridge programmed is Smith-Waterman.
We currently can perform ~20 Billion Smith-Waterman steps per second per
HC-62 which translates into 1.5 days for the entire x vs y chromosomes (30M
X 140M). 

Any questions let me know

Kent Gilson
KGilson at starbridgesystems.com

Star Bridge Systems in Salt Lake City set this up in early 2002 for the US
National Cancer Institute.


You can find more examples on their web site.

Bill Harman,
P - (801) 572-9252  F - (801) 571-4927
wharman at prism.net

------ High Performance Computing Solutions ------

-----Original Message-----
From: bio_bulletin_board-bounces+wharman=prism.net at bioinformatics.org
[mailto:bio_bulletin_board-bounces+wharman=prism.net at bioinformatics.org] On
Behalf Of Deepan Chakravarthy
Sent: Monday, October 16, 2006 10:56 AM
To: General Forum at Bioinformatics.Org
Cc: anand at novaglobal.com.sg; henny at novaglobal.com.sg;
ivanho at novaglobal.com.sg
Subject: [BiO BB] Smith-Waterman on FPGA

 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. 
Deepan Chakravarthy N

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