[Biojava-l] odds ratio

[mark.schreiber at novartis.com]

>Hi,
>
>I am trying to set up an HMM wth a few states. I have a background
>state with background distribution. For the rest of the states, I set
>up the distribution and then use the setNullModel to set the  null
>distribution to the background distribution. Am I doing the right
>thing?

Sounds correct.

>The reason why I am asking is when I tried using the forward backward
>algorithm, the scores of the state that I am interested in at each
>site is greater than 2000. I would expect some sites to have a number
>less than 1 to indicate that it is more likely to be in the null
>distribution, or am I doing something totally wrong here?

If you used an odds scoring function then you have done things correctly. 
Sounds wierd.

- Mark