State-transition diagram of the GHMM for GlimmerHMM. The dashed line in the middle separates the positive strand and negative strand portions of the model. Each state in the GHMM is implemented as a separate submodel, such as a weight array matrix or an IMM (interpolated Markov models).
Allen et al. Genome Biology 2006 7(Suppl 1):S9 doi:10.1186/gb-2006-7-s1-s9