Viterbi                                                                Forward-Backward Amino acid HMM RMHMM PRMHMM HMM RMHMM PRMHMM A 56.03 56.03 57.69 61.68 65.93 62.72 C 53.15 54.5 51.71 58.7 58.62 60.44 D 47.1 57.81 49.92 53.07 66 54.12 E 48.77 60.56 51.32 53.93 66.71 56.72 F 52.47 55.98 54.89 57.79 61.89 60.17 G 51.29 62.98 54.84 57.14 68.66 57.99 H 51.31 53.36 54.52 56.94 61.02 59.46 I 61.46 59.93 57.34 67.97 66.22 68.1 K 47.94 57.63 50.14 54.06 64.89 56.27 L 47.81 58.52 49.98 52.9 64.25 55.86 M 50.27 54.49 51.7 55.36 63.97 58.04 N 47.8 57.52 48.89 53.91 64.86 56.38 P 59.69 59.99 60.43 65.41 68.79 66.47 Q 51.43 57.82 53.78 57.91 64.69 60.28 R 52.04 56.48 53.57 58.32 64.27 61.08 S 54.59 53.81 56.01 60.36 61.18 62.89 T 53.64 53.93 55.26 59.8 60.7 63.29 V 53.64 59.39 55.89 60.01 65.23 62.13 W 55.35 53.38 57.85 61.25 59.97 63.4 Y 49.78 53.75 50.36 54.53 60.03 57.53 TOTAL 52.28 57.07 53.77 58.05 63.95 60.16

Table 4: The accuracy of the protein secondary structure prediction of each amino acid for HMM, RMHMM and PRMHMM using Viterbi and Forward-Backward algorithms applying 5 fold cross-validation.