[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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