[Biojava-l] HMM's - Attempting some fancy stuff

[Todd Riley]

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
>
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