## Figure 1.
A simple HMMer profile HMM model visualized by HHMVE. S: start state, N: N-terminal insertion state, B: beginning state of the core of
HMM, M: matching state (square), D: deletion state (yellow circle), I: insertion state
(pink diamond), E: ending state of the core of HMM, J: jump state from E to B to allow
domain duplication, C: C-terminal insertion state, T: terminal state. This example
model has three M states (M1-3), three D states (D1-3), and two I states (I1-2). Squares
(M states) and diamonds (N, I, C, J states) are emission states that can generate
symbols according to emission probabilities. Circles (S, B, D, E, T) states are dummy
states that do not generate symbols. The connectivity (directed edge) between two
states denotes a possible transition. The number associated with an edge is the transition
probability. The connectivity between B, M, D, I, E states is similar as the traditional
profile HMM [1] except that B can jump to any M states and M states can jump to E. These new connectivity
allows the local alignment with respect to HMM.
Dai and Cheng |