[BiO BB] Fast HMMer and BLASTN code

Martin Gollery marty.gollery at gmail.com
Wed Nov 16 12:53:11 EST 2005

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!


On 11/16/05, Joe Landman <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 and our photos at http://photos.scalability.org .
> --
> 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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Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
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