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 <[EMAIL PROTECTED]> 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. �douard-Montpetit > Montr�al (Qu�bec) H3T 1J4 > > Tel: (514) 343-6111 x.4066 > Courriel: [EMAIL PROTECTED] > =================================================================== > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > 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 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
