[BiO BB] Smith-Waterman on FPGA

[William Harman]

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.

http://www.starbridgesystems.com/news/43/national-cancer-institute-nci-purch
ases-starbridge-hypercomputer-to-accelerate-genome-data-research

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

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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