[BiO BB] RE: Hardware implemntation of HMMs

[Martin Gollery]

Yes, they do. They accelerate HMMer models, not SAM. 

Marty

Quoting Eitan Rubin <Eitan.Rubin at weizmann.ac.il>:

> 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
> ----- Original Message ----- 
> From: <bio_bulletin_board-request at bioinformatics.org>
> To: <bio_bulletin_board at bioinformatics.org>
> Sent: Saturday, September 13, 2003 6:01 PM
> Subject: BiO_Bulletin_Board digest, Vol 1 #521 - 1 msg
> 
> 
> > When replying, PLEASE edit your Subject line so it is more specific
> > than "Re: BiO_Bulletin_Board digest, Vol..."
> >
> >
> > 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
> > >
> > >
> > >
> > > ---------------------------------
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> >
> >
> > 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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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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