Figure 1

Final 36 hidden states HMM learned using DSSP assignment. Upper part: hidden state graph. Only transitions associated with probabilities greater than 0.1 are shown. The larger the transition probabilities the thicker the arrows. States are colored according to their amino acid preference (hydrophobic versus hydrophilic). Purple state indicates no strong amino acid preference and red states strongly favor glycine. The two groups of coil states (c1, c6, c12, c5, c4) in green and (c3, c2, c8, c10, c9) in red are discussed in the text. For periodic secondary structures, helix and strand, the entry and exit states are indicated by different symbols. Lower part: amino-acid propensities of each hidden state. Propensities are measured by log-odd scores. The propensity score of amino-acid a for state s is given by: $S=lo{g}_2\frac{P(a|s)}{f(a)}$, with P(a | s) the emission probability of amino-acid a in state s and f(a) the background frequency of a in the dataset. A score equal to 1 means that the amino-acid is twice as frequent in state s as in the whole dataset.