Ian, I'd be happy to run benchmarks for you on the various hardware that I have access to but I cannot use WU-Blast as it is non-free to people who are not in academia or at a nonprofit institution. -Chris Ian Korf wrote: > > (1.1) The first test is to search the Pfam globin family against > itself using default parameters. There are 1203 sequences in the > family. You can find the file at http://dna.cs.wustl.edu/globins.gz. > I'm using WU-BLAST with the following command line. > > time blastp globins globins V=1203 B=1203 cpus=1 filter=seg+xnu > > /dev/null > > Notes: I'm setting the CPU count to 1. Also, although I'm using > WU-BLAST here, if more people are using NCBI-BLAST, I'd like to report > that instead. This is not a bake-off of NCBI-BLAST vs. WU-BLAST. > People have their preferences, and I'm only going to include one or > the other in the book. > -- Chris Dagdigian, <dag@sonsorol.org> Bioteam.net - Independent Bio-IT & Informatics consulting Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193 PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net