Viterbi                                                      Forward-Backward Amino acid HMM MHMM HMM MHMM A 56.03 57.69 61.68 61.56 C 53.15 55.29 58.7 59.75 D 47.1 49.6 53.07 54.33 E 48.77 51.53 53.93 57.18 F 52.47 55.19 57.79 59.45 G 51.29 54.78 57.14 58.15 H 51.31 54.89 56.94 59.41 I 61.46 57.18 67.97 68.1 K 47.94 50.46 54.06 57.03 L 47.81 50.27 52.9 55.82 M 50.27 51.99 55.36 57.56 N 47.8 49.95 53.91 56.71 P 59.69 61.04 65.41 66.61 Q 51.43 53.99 57.91 59.5 R 52.04 54.38 58.32 59.87 S 54.59 56.42 60.36 62.44 T 53.64 55.33 59.8 63.05 V 53.64 55.85 60.01 60.64 W 55.35 57.95 61.25 62.36 Y 49.78 51.04 54.53 57.85 TOTAL 52.28 54.24 58.05 59.87

Table 2: The accuracy of the protein secondary structure prediction for HMM, RMHMM and PRMHMM using Viterbi and Forward-Backward algorithms applying 5 fold cross-validation.