[Biojava-l] DP forward algorithm

Ren, Zhen zren@amylin.com
Fri, 10 Jan 2003 07:54:16 -0800

Hi, there,

The three main DP operations are Forwards, Backwards and Viterbi. Forwards and Backwards calculate the probability of the sequences having been made in any way by the model. Viterbi finds the most supported way that the sequence could have been made.

I have seen the Dice example that demonstrates how to use Viterbi algorithm.  And I guess it would be the similar way to use Forward algorithm.  However, it's not like what I thought.  Can someone give me a direction how to use the Forward algorithm in DP class?  Is any tutorial regarding DP and HMM available?  More documentations about DP and HMM classes in BioJava other than Javadocs are also very helpful.

Thank you.