[Bioclusters] Parallel Bioinformatics Applications

[Christopher Dwan]

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
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