[Biodevelopers] Re: Four Questions Relating to HMMer

[Shawn O'Connor]

> One of the big questions I have is why there is no fast SSE-2 version 
> (we have a cluster of Pentium IV's here we'd like to try running it on).  > http://bioinformatics.org/pipermail/biodevelopers/2003-January/000151.html > claims that it's a lack of a  vector max instruction ...
> Can someone point me to the bleeding edge performance of HMMer on x86?

There are a few SSE implementations of HMMER, one is LDhmmer
from Logical Depth which has accelerated versions of hmmpfam
and hmmsearch, and another I'm aware of is SPSpfam from
Southwest Parallel which as far as I know is only hmmpfam. 

http://logicaldepth.com/ldhmmer/
http://www.spsoft.com/pfampages/ 

I'm interested in hearing more about various HMMER workflows
as well. 

Shawn O'Connor
shawn at logicaldepth.com
http://logicaldepth.com/