Cs 262: Computational Genomics Professor Serafim Batzoglou Lecture 8: Pair Hmms and Protein Alignment Finite State Automaton for Alignment
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چکیده
We have labeled every transition in the model with a score. Transitions to state M indicate letter-to-letter correspondences, so they are labeled with s(xi, yj) corresponding to the substitution score for replacing xi with yj. We know which i and j to use, based on the current sum of +1’s for x and y thus far. We label every transition from M to a gap state (I or J) with the gap initiation penalty -d, and we label each transition from a gap state to itself with the gap extension penalty –e.
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