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
