Figure 2
From: Probabilistic approaches to alignment with tandem repeats
SFF (sunflower field) model. A pair hidden Markov model for alignment with tandem repeats. Each submodel Ri,α (left) is a circular profile hidden Markov model emitting tandem copies of the motif in one sequence. State M j is the match state generating j th symbol of the motif, state I j allows insertions between symbols j and j + 1 of the motif, and states D j and D j′ allow to skip state M j . States s and e designate the entry and exit points from the submodel. The full SFF model (right) contains a standard three-state PHMM with states M, I X and I Y , and two submodels Ri,X, Ri,Y for each motif i. States and submodels with subscript X and Y generate symbols in the respective sequence X or Y only.