HMM state transitions. An example of a typical HMM state transition diagram. This HMM jointly models background sequence and binding sites from a gapped PWM of length 7. State 0 is the background state. The two arms leading out from state 0 generate binding sites on the positive and negative strands. States 1 and 14 are the first states for binding sites generated in the positive and negative direction respectively. Similarly states 5 and 12 represent the optional base for binding sites generated in the positive and negative direction respectively. When training the HMM various parameters are tied so that they are always equal. For example, the transition parameter from state 0 to state 1 is tied to the parameter for the equivalent transition to state 14. This ensures binding sites are equally likely on both strands of DNA. Similarly emission parameters are tied to ensure binding sites on the negative strand have a distribution that is the reverse complement of the distribution of the binding sites on the positive strand.
Reid et al. BMC Genomics 2010 11:30 doi:10.1186/1471-2164-11-30