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.
<br><br>None of these can touch an accelerator, but then, they are much cheaper!<br><br>Marty<br><br><div><span class="gmail_quote">On 11/16/05, <b class="gmail_sendername">Joe Landman</b> <<a href="mailto:landman@scalableinformatics.com">
landman@scalableinformatics.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi folks:<br><br> I want to announce that we appear to have the fastest HMMer and
<br>BLASTN builds and benchmarks for AMD Opteron architecture machines. Our<br>HMMer benchmarking gives us a 2x advantage over the commonly downloaded<br>binaries, and 2.5x on some customer tests. The blastn binaries give us
<br>about 22-24% advantage over the code downloadable from NCBI.<br><br> These builds are immediately available from Scalable Informatics and<br>our partners. Please contact us offline for more information. Some<br>benchmark snapshots may be seen at
<a href="http://www.scalableinformatics.com">http://www.scalableinformatics.com</a> .<br><br> Joe<br><br>ps: while we are at SC'05, you can see our blog/comments at<br><a href="http://scalability.org">http://scalability.org
</a> and our photos at <a href="http://photos.scalability.org">http://photos.scalability.org</a> .<br><br>--<br>Joseph Landman, Ph.D<br>Founder and CEO<br>Scalable Informatics LLC,<br>email: <a href="mailto:landman@scalableinformatics.com">
landman@scalableinformatics.com</a><br>web : <a href="http://www.scalableinformatics.com">http://www.scalableinformatics.com</a><br>phone: +1 734 786 8423<br>fax : +1 734 786 8452<br>cell : +1 734 612 4615<br><br>_______________________________________________
<br>Bioinformatics.Org general forum - <a href="mailto:BiO_Bulletin_Board@bioinformatics.org">BiO_Bulletin_Board@bioinformatics.org</a><br><a href="https://bioinformatics.org/mailman/listinfo/bio_bulletin_board">https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
</a><br></blockquote></div><br><br clear="all"><br>-- <br>-- <br>Martin Gollery<br>Associate Director<br>Center For Bioinformatics<br>University of Nevada at Reno<br>Dept. of Biochemistry / MS330<br>775-784-7042<br>-----------