A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model

Figure 1

The ComSPS HMM state transition diagram. Emission states are represented by shaded circles. The auxiliary states are represented by circles, which are only used to model the structure (not to emit specific bases). and are the initiating and terminating states of the model, respectively. Only the transition probabilities marked by dotted lines need estimating in the model training.