[BiO BB] Accelerating HMM in FPGA

Valery Miftakhov valery at biozak.com
Thu Jan 15 19:33:01 EST 2004

Hi All,

I have just stumbled across this older post from one of the members of 
this group, Venu Kobe, and I am interested in the progress that you, 
Venu, and possibly anyone else had in accelerating HMM in FPGA.

Please let me know.

Valery Miftakhov, Ph.D. -- (650)-906-0477

Hello everyone,
I am graduate student in computer engineering doing my thesis in the following topic:
"Matching Protein sequences with HMM models in FPGAs ( Field Programmable Gate Arrays ) using Run Time Reconfiguration"
If you are familiar with Decypher tool from TimeLogic, my work involves something similar to that.  Decypher is a very comprehensive and expensive tool and sure it does deliver excellent performance compared to the software tools such as HMMR, SAM or the other tools. My work falls in between the software solution and that of Decypher.
Specifically, when developed my tool would be considerably faster than that of the software tools currently available and also be affordable at a fraction of the cost of using Decypher. 
I have just started digging into Bioinformatics and have read quite a number of papers and all, but I am still a little confused and would like any comments or suggestions from you:
1) Does my tool make any sense at all? 
2) What is the current customer base like for this technology? 
3) What sort of companies do the work of matching protein/DNA sequences with existing models? 
4) Is there a need for a less comprehensive and less expensive tool as opposed to Decypher for customers who want to get it done a lot less cheaper but wouldnt mind the extra penalty in performace ( ofcourse will be very much better than that of the software searching)
5) Any comments, questions, suggestions?
6) Any pointers for me in terms of websites or resources.
I would very much appreciate your comments

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