Figure 3.

A representation of the matrix produced by the forward algorithm modified to incorporate some prior information. We have a (hypothetical) model, which consists of 12 states, with 3 labels I, M, O corresponding respectively to states modelling the intracellular, transmembrane and extracellular parts of the sequence. The likelihood of sequence x (8 residues), is calculated incorporating the prior information that residues 3 and 4 are transmembrane, residue 1 is extracellular and residue 8 is intracellular.