Dear list, I'm Daniel, a CS student at Stanford, and I've recently become quite interested in exploring HMMer and its related algorithms. I've got 4 questions here: I've taken a look at the AltiVec implementation, and heard that Erik Lindahl has worked on a second revision of his AltiVec implementation. (here http://lindahl.sbc.su.se/software/altivec/altivec-hmmer,-version-2.html) Does anyone know actual performance numbers or where I could test code snippits? 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). The article here http://bioinformatics.org/pipermail/biodevelopers/2003-January/000151.html claims that it's a lack of a vector max instruction, but that doesn't seem like the whole story, is it? Can someone point me to the bleeding edge performance of HMMer on x86? I've been going through the documentation for HMMer and have found a few hints at the details of hmmer usage, but I'd be quite interested in knowing the steps in a real-world HMMer workflow. Are hundreds of queries produced at once? or is generally a single carefully aligned hmm model fed through a rather largish database to produce a result an hour later. Would speeding this computation up on an x86 help the average biologist in the lab: what speedup would actually be notable? I've found some Pfam databases online-- is there a more comprehensive one that I can run benchmarks on, for instance, to study the SSE version produced in the Jan 2003 post? Anyhow thanks in advance, I'd appreciate answers to any of these questions at all :-) Daniel