I think you could do a palindrome as a push-down automaton or similar. Alternatively you could do something like a HMM with emission duration as in Borodovsky's GeneMarkHMM programs but that would require a lot of new code for the DP library (good to have though).
To use a Dirichlet mixture as your background you could calculate one and give it to a Distribution although it might be best to implement the Distribution interface with a class that generates one for you. To go to higer order models you just need a higher order alphabet (http://biojava.org/wiki/BioJava:Cookbook:Alphabets:CrossProduct) and possibly use an OrderNDistribution for background and emission (http://biojava.org/wiki/BioJava:CookBook:Distribution:Custom) - Mark Todd Riley <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 03/24/2006 07:04 AM To: Francois Pepin <[EMAIL PROTECTED]> cc: [email protected], Mark Schreiber/GP/[EMAIL PROTECTED] Subject: Re: [Biojava-l] HMM's - Attempting some fancy stuff Yes, I agree that the palindromes are not always identical. However, often my unaligned training data is not complete enough to train the model well without some simplification. So far, I have been using Cross-validation, sensitivity, and specificity to determine the effectiveness of this simplification approach. -Todd Francois Pepin wrote: >>1. Many of the TFBS sites that I am modeling are palindromic or >>repetitive. I wish to associate transition and emission distributions >>(as prior knowledge) during training in order to enforce a palindromic >>and/or repetitive pattern and thus also greatly reduce the parameter space. >> >> > >Just as a note, we haven't found this to be ideal, if you have >sufficient training data. It is often the case that one of the >palindromes is more conserved than the other, and you would treating >them the same way. > >Of course, it depends how much of an in-depth study you'll want to be >doing. > >Francois > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
