Figure 3

A pair-HMM for pairwise sequence alignment. A pair-HMM is used for alignment of loop regions and calculation of the posterior probabilities in score function. The state M has emission probability distribution $p_{x_i{y}_j}$ for emitting an aligned pair x _i and y _j . The state I _x has distributions $q_{x_i}$ for emitting symbol x _i against a gap. The state I _y has distributions $q_{y_j}$ for emitting symbol y _j against a gap. The parameters δ and ε are the state transition probabilities.