[Biojava-l] Anyon has ever search for CpG Islands with BioJava?

[Sylvain Foisy]

Hi,

Sorry for the hand holding question. I am trying to wrap the output of a
Perl script that finds CpG islands (cpgi130.pl) using Runtime.exec with
little success. Has anyone ever built a class that can find CpG islands in
Sequence objects and build features with RangeLocations?

Other solution: has anyone ever try to write a wrapper that would use the
output of any program of the EMBOSS suite? It has some CpG island finding
software.

Anyhelp would be much appreciated

P.S.: there has been a call for an algorithm repository on Usenet. Would it
be possible/interesting to create such a repository for classes built with
BioJava that could be of interest to other rookies like me.

Just an idea...

Sylvain


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Sylvain Foisy, Ph. D.
Directeur - operations / Project Manager
BioneQ - Reseau quebecois de bio-informatique
U. de Montreal / Genome-Quebec

Addresse postale:

Departement de biochimie
Pavillon principal
2900, boul. Édouard-Montpetit
Montréal (Québec) H3T 1J4

Tel: (514) 343-6111 x.4066
Courriel: sylvain.foisy at bioneq.qc.ca
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