I have implemented Viterbi algorithm, and I need to implement the forward algorithm but I can't understand how does it work.
I have read a lot of slides and sick of math notation at this point. It does not help. I need something that in plain English explains the Forward algorithms.Can you provide a short explanation how is forward algorithm done?
Assume we have the following profile HMM and we want to use Forward algorithm to align sequence ACACAGC to this profile . Can anyone show me the way ??
The forward algorithm allows you to compute the probability of a sequence given the model. This is obtained by summing over all possible state paths that can give rise to this sequence. This could be done by enumerating all the paths but this is not very efficient so instead the forward algorithm uses dynamic programming. For this, you set up a dynamic programming matrix where the rows represent the states and the columns the nucleotides of the sequence. Then you fill up the matrix starting from the top left corner and going by column using the recursive formula: probability of emitting the current nucleotide (column) from the current state (row) times the sum of, for all previous nucleotides and all other states, the probability of the nucleotide in that state (that's were the recursion is, this is the sum of probabilities over all paths giving the sequence up to this point) times the probability of transitioning to the current state.
I compute the probability for the first three nucleotide's (ACA), then I try to compute the probability for the fourth nucleotide but I do not know how
could you please show me the final matrix so I can check if I understand you well
Sounds too much like homework. Post your solution and we'll check it.
it is not homework, I just interested in this algorithm.
I compute the probability for the first three nucleotide's (ACA), then I try to compute the probability for the fourth nucleotide but I do not know how
Is the final answer equal 0.0323