# This file is the result of combining several RDB files, specifically # T0358.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0358.t2k.stride-ebghtl.rdb (weight 1.24869) # T0358.t2k.str2.rdb (weight 1.54758) # T0358.t2k.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0358.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0358 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0358.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 14 # # ============================================ # Comments from T0358.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0358 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0358.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 14 # # ============================================ # Comments from T0358.t2k.str2.rdb # ============================================ # TARGET T0358 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0358.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 14 # # ============================================ # Comments from T0358.t2k.alpha.rdb # ============================================ # TARGET T0358 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0358.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 14 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0803 0.0270 0.8928 2 T 0.1827 0.0447 0.7726 3 Q 0.1972 0.1252 0.6775 4 S 0.1894 0.1857 0.6250 5 V 0.2945 0.1625 0.5430 6 L 0.2941 0.0998 0.6061 7 L 0.1372 0.0358 0.8270 8 P 0.0702 0.0626 0.8672 9 P 0.0618 0.0577 0.8805 10 G 0.0607 0.0400 0.8993 11 P 0.0828 0.0751 0.8421 12 F 0.1398 0.1035 0.7567 13 T 0.1042 0.2135 0.6823 14 R 0.0088 0.9222 0.0690 15 R 0.0062 0.9435 0.0502 16 Q 0.0052 0.9532 0.0416 17 A 0.0051 0.9560 0.0389 18 Q 0.0057 0.9558 0.0385 19 A 0.0055 0.9537 0.0407 20 V 0.0061 0.9523 0.0416 21 T 0.0103 0.9353 0.0544 22 T 0.0177 0.8712 0.1111 23 T 0.0458 0.7489 0.2053 24 Y 0.1382 0.5415 0.3203 25 S 0.1280 0.3645 0.5076 26 N 0.2047 0.2250 0.5704 27 I 0.3998 0.1457 0.4545 28 T 0.5467 0.0885 0.3648 29 L 0.4537 0.1487 0.3976 30 E 0.3514 0.1241 0.5245 31 D 0.2160 0.1009 0.6831 32 D 0.1642 0.0423 0.7935 33 Q 0.1004 0.0797 0.8199 34 G 0.1162 0.1116 0.7723 35 S 0.2364 0.1013 0.6623 36 H 0.6116 0.0421 0.3463 37 F 0.7974 0.0131 0.1895 38 R 0.8866 0.0099 0.1035 39 L 0.9173 0.0040 0.0787 40 V 0.9132 0.0042 0.0825 41 V 0.8780 0.0067 0.1153 42 R 0.8120 0.0082 0.1798 43 D 0.3307 0.0175 0.6518 44 T 0.0508 0.1186 0.8305 45 E 0.0627 0.0302 0.9071 46 G 0.1106 0.0321 0.8573 47 R 0.4035 0.0153 0.5812 48 M 0.8640 0.0052 0.1308 49 V 0.8799 0.0073 0.1127 50 W 0.9006 0.0049 0.0945 51 R 0.8394 0.0116 0.1490 52 A 0.7649 0.0180 0.2171 53 W 0.6455 0.0318 0.3226 54 N 0.4646 0.0386 0.4968 55 F 0.2139 0.0532 0.7329 56 E 0.0969 0.0463 0.8567 57 P 0.0322 0.1759 0.7919 58 D 0.0318 0.1489 0.8193 59 A 0.0509 0.3155 0.6336 60 G 0.0344 0.3744 0.5912 61 E 0.0404 0.6150 0.3447 62 G 0.0438 0.6955 0.2607 63 L 0.0494 0.8070 0.1436 64 N 0.0509 0.8338 0.1153 65 R 0.0452 0.8684 0.0864 66 Y 0.0868 0.8247 0.0885 67 I 0.0927 0.7887 0.1186 68 R 0.0889 0.7086 0.2025 69 T 0.0640 0.5689 0.3672 70 S 0.0715 0.2623 0.6662 71 G 0.0867 0.0904 0.8229 72 I 0.2468 0.0909 0.6622 73 R 0.2955 0.0881 0.6164 74 T 0.2002 0.1132 0.6866 75 D 0.1207 0.1403 0.7390 76 T 0.0688 0.3612 0.5700 77 A 0.0601 0.6225 0.3174 78 T 0.0640 0.6904 0.2456 79 R 0.0705 0.7126 0.2169 80 L 0.0716 0.7234 0.2050 81 E 0.0722 0.6781 0.2497 82 H 0.0711 0.6112 0.3177 83 H 0.0899 0.4640 0.4461 84 H 0.0902 0.3425 0.5672 85 H 0.0805 0.2032 0.7163 86 H 0.0702 0.0985 0.8314 87 H 0.0453 0.0377 0.9170