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Sequence Matching & HMM Modeling in Hardware (FPGA)

xfpgas vkode78 at yahoo.com
Mon Sep 15 10:58:29 EST 2003

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 on a very small scale.  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? or Should I try to solve
another problem in Bioinformatics in Hardware?
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)What are the pressing needs in terms of Computation involved in
BioInformatics right now?
6) Any comments, questions, suggestions?
7) Any pointers for me in terms of websites or resources.

I would very much appreciate your comments


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