Figure 3
From: Probabilistic approaches to alignment with tandem repeats
TANTAN-like repeat model for repeat motifs of length up to K = 4. (a) Model by Frith[18] representing one tandem repeat without indels. States s and e are silent, state R k has emission table in which symbol at position i depends on symbol at position i - k. (b) Full model by Frith[18] allows insertions using states I1, … Ik-1 and deletions using silent states D1, …, D K . Our modification includes states P1 … P K for the first occurrence of the motif. (c) Full pair HMM consists of two copies T X and T Y of the model from part (b), one for each input sequence, and the traditional three-state pair HMM for non-repeat regions.