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

[Matthew Pocock]

Hi Sylvain,

I wrote an HMM for finding cpg islands using biojava,
but never perameterised it. If you're interested (and
have a training set), I'd be happy to throw the code
in your direction.

Matthew

 --- Sylvain Foisy <sylvain.foisy at bioneq.qc.ca> wrote:
> 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
> 
> 
>
===================================================================
> 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
>
===================================================================
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org
> http://biojava.org/mailman/listinfo/biojava-l 

__________________________________________________
Do You Yahoo!?
Everything you'll ever need on one web page
from News and Sport to Email and Music Charts
http://uk.my.yahoo.com