[Bioperl-l] bioperl

Jason Stajich jason.stajich at duke.edu
Mon Jan 23 22:57:47 EST 2006

On Jan 19, 2006, at 6:36 PM, Dr. Christoph Gille wrote:

> Hi Torsten,
> perhaps Sopma is not the best choice as a test case for bringing  
> perl and
> java together. It is not a convincing example because people would  
> ask why
> not
> contacting the server directly from java and why taking the hazzard  
> with
> perl installation.
> I want to demonstrate that BioPerl programs can well work together  
> with
> STRAP/Biojava with the wrapper I am  just developing but I need a  
> suitable
> example program.
> What I consider is a sophisticated non-interactive Bioperl program  
> that
> performs some kind of useful computation on a protein sequence, or an
> alignment or a protein 3D structure.
> Do you know of something appropriate ?
> It does not matter if the program is complex or contains C/C++ as  
> long as
> it can be automatically installed without user interaction.

PAML/Codeml, PHYLIP programs Neighbor, Seqboot, ProtDist, ProtPars,  
require some file formatting that but might still be criticized as  
not sufficiently difficult to brave the hazards of installing perl  
modules.  Simpler things like MUSCLE, TCOFFEE, BLAST, FASTA/SSEARCH  
might also be good choices.

> Many thanks
> Christoph
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Jason Stajich
Duke University

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