HMM extension

[tianyu-lu]

An idea for extending DNA PACman for HMMs:

A) Start from [0,0], choose in {A,C,T,G} uniformly. Then just do a double for loop going through each square that's not a wall. For position [i,j], sample from {A,C,T,G} with probabilities given by the transition probabilities table for nucleotide at [i,j-1]. If that's a wall, look at [i-1,j]. Otherwise leave blank for now.

B) Then start from the bottom right corner [m,n], repeat the above but instead first look at [i,j+1]. If that's a wall, look at [i+1,j].

Alternate between steps A and B until all nonwall cells are filled.

[HussainAther]

i'll copy this to the other issue.