Fig 1.

(A) Structural representation of a protein inserted into a membrane with several segments traversing the bilipid layer. (B) Example of an HMM process. The process starts with a hidden state, in this case I (Inside), M (Membrane), or O (Outside), which emits (green arrow) an observed state (an amino acid in 1 letter code). Then, it transitions to the next hidden state (orange arrow), which emits the next observed state, and so on. (C) Graph representation of the transition probability matrix of the HMM. The circle nodes represent the hidden states; the arrows between hidden states are transition probabilities. The emission probabilities were omitted from the graph for simplicity (S5 File). HMM, Hidden Markov Model.