[Bioclusters] help with benchmarks etc.

chris dagdigian bioclusters@bioinformatics.org
Mon, 23 Sep 2002 11:40:37 -0400


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.


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>
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