[Biojava-l] Can anyone help me with MarkovModels?

[Oscar Lopes]

Hi!

I'm working with HMMs in ORF/Gene finding. A few days ago I defined a HMM
relatively big (900 transitions and a lot of states). After
initialization, I tried to apply Viterbi algorithm to a sequence, but I
kept getting null pointer exceptions inside biojava classes. I also tried
to apply
Forward ans Backward algorithms, but I only got NaN's. Some of the states
only emmit one symbol, so I defined different alphabets for these states,
but instead of null pointer exception, I've got Illegal symbol exception.

I wonder if there is a problem with HMM classes, since this kind of
situation shouldn't occur. Is there a better solution, as some of the
states emmit only one symbol?

I'm using biojava version from CVS, a DNA alphabet, and I'm building the
HMM as explained in the tutorial using SimpleEmissionState,
SimpleMarkovModel, etc. If necessary, I can send some of my files.

I would appreciate any help, since this work is for my degree thesis and
I'm getting nervous :P

Thanks in advance.

Oscar Lopes

--
Oscar Manuel Baptista Lopes - oscar at gauss.inesc.pt
Knowledge Discovery & BioInformatics - http://algos.inesc-id.pt/kdbio/
Departamento Engenharia Informatica - http://www.dei.ist.utl.pt/
Instituto Superior Tcnico - http://www.ist.utl.pt/