Figure 1.

An example GHMM topology. Diamonds represent signal states (for fixed-length features) and circles represent content states (for variable-length features). Allowable transitions are shown with arrows. ATG = start codon, TAG = stop codon, GT = donor splice site, AG = acceptor splice site, N = intergenic region, I = intron, E_init = initial exon, E_int = internal exon, E_fin = final exon, E_sng = single exon gene. The denoted machine operates by transitioning stochastically from state to state, emitting a gene feature of a particular type upon entering a given state.