[BiO BB] RE: Hardware implemntation of HMMs

Eitan Rubin Eitan.Rubin at weizmann.ac.il
Sat Sep 13 18:23:21 EDT 2003


Hi,

  As far as I know, Compugen sells hardware accelerators for HMMs (see
http://www.cgen.com). Their website specifically mentions HMMs acceleration.

  Eitan
------------------------------------------------------------------------
Eitan Rubin, PhD
Head of Bioinformatics and Biological Computing
Dept. Biological Services
Weizmann Institute of Science
Tel: +972-8-9343456
Fax: +972-8-9346006
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Sent: Saturday, September 13, 2003 6:01 PM
Subject: BiO_Bulletin_Board digest, Vol 1 #521 - 1 msg


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> Today's Topics:
>
>    1. Re: Implementing HMM models in Hardware (FPGA) (Martin Gollery)
>
> --__--__--
>
> Message: 1
> Date: Fri, 12 Sep 2003 10:14:36 -0700
> From: Martin Gollery <mgollery at unr.edu>
> To: bio_bulletin_board at bioinformatics.org
> Subject: Re: [BiO BB] Implementing HMM models in Hardware (FPGA)
> Reply-To: bio_bulletin_board at bioinformatics.org
>
> Hi Venu,
>   Yes, this idea makes sense. Anyone who uses InterProscan wishes it were
> faster! The current customer base includes all the big genome centers,
> universities, many biotechs and larger Pharmas. Other people have done
projects
> in the field- Kestral at UCSC has been around for years, I don't know if
it has
> been updated recently. Hokiegene out of Virginia is a newer system that
shows
> great performance. There are several other commercial ventures that are in
> stealth mode right now.
>    HMM's really lend themselves well to acceleration of this type. Perhaps
you
> could focus on accelerating SAM instead of HMMer, as many people prefer it
and
> TimeLogic, Compugen and Paracel do not accelerate SAM. Also, nobody (to my
> knowledge) has accelerated ClustalW, so this might be something else to
> consider.
>
> Best of luck! Sounds like an interesting project!
>
> Marty
>
>
> 3. Quoting Venu Kode <vkode78 at yahoo.com>:
>
> > 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
> >
> > TIA
> > Kode
> >
> >
> >
> > ---------------------------------
> > Do you Yahoo!?
> > Yahoo! SiteBuilder - Free, easy-to-use web site design software
>
>
> Martin Gollery
> Associate Director of Bioinformatics
> University of Nevada at Reno
> Dept. of Biochemistry / MS330
> New phone number! 775-784-7042
>
>
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