Re: Parallel Bioinformatics Applications
Christopher Dwan <[email protected]>
| Newsgroups | gmane.science.biology.informatics.clusters |
|---|---|
| Message-ID | <[email protected]> |
The most widely used application in bioinformatics is BLAST (http:// www.ncbi.nlm.nih.gov/blast/). It's a trivially parallelizable similarity search. There is a good MPI version here (http:// mpiblast.lanl.gov/). ClustalW-MPI is a parallel version of a popular tool for creating alignments of multiple sequences. (http://web.bii.a-star.edu.sg/ ~kuobin/clustalg/) MrBayes is phylogeny program which can be built with MPI (http:// mrbayes.csit.fsu.edu/). There are others, but those are my favorite three. There are no widely accepted standard benchmarks in bioinformatics, two systems people have published in the past are: * BBS - http://www.scalableinformatics.com/metadot/index.pl?iid=2194 * IBT - http://web.bioteam.net/metadot/index.pl?iid=2378 Both were designed to be run on a single machine, rather than a cluster or in a parallel environment, last time I checked. Good luck! -Chris Dwan On Jun 19, 2006, at 5:50 AM, Gul Aftab wrote: > Hi All! > Recently we have built a computational cluster in our > university for academic research purpose. It is a linux based cluster > performing at 245 GFlops/sec. Now i want to run some real life > applications specially bioinformatics applications. Can anyone suggest > some applications (Parallel linux applications) which i can run on my > cluster. > > Thanks, > Gul Aftab > _______________________________________________ > Bioclusters maillist - [email protected] > https://bioinformatics.org/mailman/listinfo/bioclusters