I've been working on this for few hours and no luck. I'd appreciate any help.
Based on the Viterbi algorithm, marginal probability of a sequences being generated by a given HMM model with the Forward algorithm, I'm trying to calculate both, the most probable path-Viterbi- as well as the marginal probability of observing the sequence “ILDE”, for the model defined below.
a. The model has two possible states: transmembrane state (TM) and non-transmembrane state (NT)
b. The state transition matrix A:
St+1 TM NT St TM 0.8 0.2 NT 0.2 0.8
a. The emission matrix E:
Amino Acids L I E D State TM 0.45 0.45 0.05 0.05 NT 0.05 0.05 0.45 0.45
Assume that transition from start state to TM or NT has equal chance 0.5.