Computational Biology - Lecture 2

Today, the second lecture studied the pair hidden Markov model for sequence alignment. Then the following steps have been taken:

• The tropicalization of the marginal probabilties leads to the optimal alignment problem. 
• The marginal probabilities are decomposed and the associated tropicalization elucidates an algorithm for optimal sequence alignment. 
• In particular, if the scores for the edit strings are neglected, the algorithm corresponds to the original algorithm of Needleman and Wunsch.