[Bioclusters] Looking for information

[Lars G.T.Jorgensen]

Here are a few more:

mpiBlast
http://mpiblast.lanl.gov/
A sequence database searching program. You give it a query sequence
and it searches a database for similar sequences.

POY
http://ftp.amnh.org/pub/people/wheeler/poy.
It builds trees of how sequences are related... (don't know how widly
used it is..). It runs on top of PVM.

BioPerl:
http://www.bioperl.org
It a Perl toolkit designed for bioinformatics. I not targeted at
clusters but it could give you a picture of some possible
applications.

Here a link to the proceedings of BOSC (Bioinformatics Open Source
Conference) 2002:
http://www.open-bio.org/bosc2002/program.html
You can proberbly find some funs things to look at there...




Philip MacMenamin <pm66@nyu.edu> writes:

> Hi Srihari, 
> 
> There is an application called interproScan that appears to fit your 
> criterea. I was talking to the author, and it has been designed to be 
> clustered. http://www.ebi.ac.uk/interpro/scan.html. 
> 
> If you can get it working on the cluster, I would be interested in knowing 
> how you did it. I tried to get it running on a linux MOSIX cluster, but 
> failed. It wont migrate the processed off the job scheduler node for
> me. 



> 
> Tell me if you decide to run InterPro. 
> 
> Good luck, 
> Philip.
> On Thursday 02 October 2003 12:25 pm, you wrote:
> > Hello list members,
> >   I am new to bioinformatics field, but not new to cluster computing. I am
> > in need of help here. I am looking for some interesting demo cluster
> > applications in the bio- field. Specifically looking for applications that
> > I can download (free or evaluation versions), compatible with Linux,
> > parallel/distributed, and those I can automate the processing via a batch
> > scheduling system. Graphical applications are also fine. If you could
> > point me to a thread in the archive similar to this topic or some URLs,
> > I'd really appreciate it.
> >
> > Thank you,
> > Srihari
> >
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> 
> 

-- 
Mvh|Regards, Lars
Graduate student 
Department of Computer Science, University of Copenhagen