[BiO BB] Fast HMMer and BLASTN code

Joe Landman landman at scalableinformatics.com
Wed Nov 16 14:17:52 EST 2005


We would be willing to do this, or ask someone else to do this if they 
are willing.

Martin Gollery wrote:
> It might be interesting to compare all the optimized HMMer codes. A 
> couple of years I wanted to compare SPSpfam to LDhmmer, but the folks at 
> Logical Depth wouldn't give me a demo of their code. Logical Depth 
> claims a 10x speedup for their code over the standard HMMer. I did test 
> SPSpfam and saw speedups of around 20X although other people have seen 
> speedups of 60x.
> 
> None of these can touch an accelerator, but then, they are much cheaper!
> 
> Marty
> 
> On 11/16/05, *Joe Landman* < landman at scalableinformatics.com 
> <mailto:landman at scalableinformatics.com>> wrote:
> 
>     Hi folks:
> 
>        I want to announce that we appear to have the fastest HMMer and
>     BLASTN builds and benchmarks for AMD Opteron architecture machines.  Our
>     HMMer benchmarking gives us a 2x advantage over the commonly downloaded
>     binaries, and 2.5x on some customer tests.  The blastn binaries give us
>     about 22-24% advantage over the code downloadable from NCBI.
> 
>        These builds are immediately available from Scalable Informatics and
>     our partners.  Please contact us offline for more information.  Some
>     benchmark snapshots may be seen at http://www.scalableinformatics.com .
> 
>        Joe
> 
>     ps: while we are at SC'05, you can see our blog/comments at
>     http://scalability.org <http://scalability.org> and our photos at
>     http://photos.scalability.org .
> 
>     --
>     Joseph Landman, Ph.D
>     Founder and CEO
>     Scalable Informatics LLC,
>     email: landman at scalableinformatics.com
>     <mailto:landman at scalableinformatics.com>
>     web  : http://www.scalableinformatics.com
>     phone: +1 734 786 8423
>     fax  : +1 734 786 8452
>     cell : +1 734 612 4615
> 
>     _______________________________________________
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> 
> 
> 
> -- 
> -- 
> Martin Gollery
> Associate Director
> Center For Bioinformatics
> University of Nevada at Reno
> Dept. of Biochemistry / MS330
> 775-784-7042
> -----------
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 734 786 8452
cell : +1 734 612 4615



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