# This file is the result of combining several RDB files, specifically # T0187.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0187.t2k.stride-ebghtl.rdb (weight 1.24869) # T0187.t2k.str.rdb (weight 1.53983) # T0187.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 T0187.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0187 # 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 T0187.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 29 # # ============================================ # Comments from T0187.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0187 # 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 T0187.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 29 # # ============================================ # Comments from T0187.t2k.str.rdb # ============================================ # TARGET T0187 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0187.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 29 # # ============================================ # Comments from T0187.t2k.alpha.rdb # ============================================ # TARGET T0187 # 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 T0187.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 29 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0766 0.0243 0.8991 2 V 0.1414 0.0306 0.8280 3 P 0.1023 0.0563 0.8414 4 D 0.0649 0.1387 0.7963 5 E 0.0101 0.7456 0.2443 6 N 0.0120 0.7801 0.2079 7 T 0.0077 0.9074 0.0848 8 I 0.0045 0.9525 0.0430 9 K 0.0044 0.9569 0.0388 10 T 0.0044 0.9560 0.0396 11 T 0.0044 0.9587 0.0369 12 R 0.0044 0.9600 0.0356 13 R 0.0044 0.9585 0.0371 14 V 0.0044 0.9575 0.0382 15 L 0.0045 0.9549 0.0406 16 E 0.0045 0.9495 0.0460 17 L 0.0053 0.9167 0.0779 18 V 0.0130 0.8662 0.1208 19 D 0.0082 0.6665 0.3252 20 Q 0.0144 0.2749 0.7107 21 L 0.0577 0.0619 0.8804 22 N 0.0516 0.0237 0.9247 23 E 0.0128 0.2729 0.7143 24 N 0.0212 0.1627 0.8161 25 D 0.1876 0.1018 0.7106 26 T 0.7884 0.0097 0.2019 27 V 0.9244 0.0038 0.0718 28 L 0.9319 0.0036 0.0645 29 F 0.9290 0.0036 0.0674 30 L 0.8857 0.0057 0.1086 31 L 0.7051 0.0168 0.2781 32 S 0.3993 0.0272 0.5736 33 G 0.1221 0.0831 0.7948 34 G 0.0663 0.2004 0.7333 35 G 0.0686 0.4189 0.5126 36 S 0.0885 0.4976 0.4139 37 S 0.1103 0.4788 0.4108 38 L 0.1843 0.3389 0.4768 39 F 0.2182 0.1700 0.6118 40 E 0.3265 0.0819 0.5916 41 L 0.2527 0.0520 0.6953 42 P 0.1715 0.0641 0.7645 43 L 0.0620 0.2606 0.6774 44 E 0.0276 0.1581 0.8143 45 G 0.0426 0.0831 0.8743 46 V 0.1932 0.0124 0.7944 47 S 0.1131 0.0124 0.8745 48 L 0.0057 0.8941 0.1002 49 E 0.0045 0.9330 0.0625 50 E 0.0049 0.9431 0.0521 51 I 0.0044 0.9523 0.0432 52 Q 0.0045 0.9521 0.0435 53 K 0.0045 0.9525 0.0430 54 L 0.0044 0.9535 0.0421 55 T 0.0045 0.9558 0.0397 56 S 0.0044 0.9572 0.0384 57 A 0.0044 0.9576 0.0380 58 L 0.0048 0.9538 0.0414 59 L 0.0052 0.9444 0.0504 60 K 0.0076 0.9074 0.0849 61 S 0.0407 0.4488 0.5105 62 G 0.0336 0.0411 0.9253 63 A 0.0620 0.0251 0.9128 64 S 0.1105 0.1175 0.7721 65 I 0.0186 0.8715 0.1100 66 E 0.0149 0.9174 0.0677 67 E 0.0194 0.9273 0.0533 68 I 0.0115 0.9351 0.0534 69 N 0.0055 0.9506 0.0439 70 T 0.0058 0.9480 0.0462 71 V 0.0060 0.9412 0.0528 72 R 0.0058 0.9294 0.0647 73 K 0.0062 0.9157 0.0780 74 H 0.0087 0.8608 0.1305 75 L 0.0151 0.7693 0.2156 76 S 0.0118 0.6966 0.2916 77 Q 0.0150 0.5923 0.3928 78 V 0.0517 0.3876 0.5608 79 K 0.0572 0.2223 0.7205 80 G 0.0450 0.3303 0.6247 81 G 0.0499 0.6209 0.3292 82 R 0.0319 0.8417 0.1264 83 F 0.0151 0.9053 0.0797 84 A 0.0112 0.9054 0.0834 85 E 0.0116 0.8811 0.1074 86 R 0.0121 0.7939 0.1940 87 V 0.0390 0.6246 0.3364 88 F 0.0728 0.3331 0.5941 89 P 0.0842 0.1577 0.7581 90 A 0.1574 0.0564 0.7862 91 K 0.2914 0.0364 0.6722 92 V 0.8386 0.0062 0.1552 93 V 0.8787 0.0085 0.1128 94 A 0.9224 0.0045 0.0731 95 L 0.9270 0.0040 0.0691 96 V 0.9212 0.0041 0.0746 97 L 0.8521 0.0160 0.1319 98 S 0.7017 0.0171 0.2813 99 D 0.3680 0.0494 0.5825 100 V 0.2199 0.0305 0.7496 101 L 0.1024 0.0616 0.8359 102 G 0.0670 0.0425 0.8905 103 D 0.1185 0.0270 0.8544 104 R 0.1043 0.0784 0.8173 105 L 0.0463 0.7054 0.2483 106 D 0.0306 0.7639 0.2055 107 V 0.0964 0.7227 0.1809 108 I 0.2536 0.4636 0.2828 109 A 0.2849 0.3096 0.4055 110 S 0.2872 0.2027 0.5101 111 G 0.1557 0.0676 0.7767 112 P 0.1402 0.1046 0.7552 113 A 0.1949 0.0958 0.7094 114 W 0.1474 0.0524 0.8002 115 P 0.1031 0.0377 0.8592 116 D 0.0963 0.0397 0.8640 117 S 0.0196 0.2477 0.7327 118 S 0.0366 0.2502 0.7133 119 T 0.0639 0.2528 0.6833 120 S 0.0074 0.8179 0.1747 121 E 0.0057 0.8476 0.1467 122 D 0.0064 0.8821 0.1114 123 A 0.0044 0.9518 0.0438 124 L 0.0044 0.9583 0.0373 125 K 0.0044 0.9584 0.0373 126 V 0.0044 0.9593 0.0364 127 L 0.0045 0.9556 0.0399 128 E 0.0048 0.9433 0.0519 129 K 0.0067 0.8760 0.1172 130 Y 0.0428 0.5594 0.3978 131 G 0.0348 0.1074 0.8578 132 I 0.0532 0.1003 0.8465 133 E 0.0790 0.1025 0.8184 134 T 0.0870 0.0342 0.8789 135 S 0.0704 0.0796 0.8500 136 E 0.0082 0.8367 0.1551 137 S 0.0080 0.8965 0.0956 138 V 0.0071 0.9412 0.0517 139 K 0.0067 0.9503 0.0430 140 R 0.0073 0.9458 0.0469 141 A 0.0067 0.9358 0.0574 142 I 0.0104 0.9052 0.0844 143 L 0.0129 0.8084 0.1787 144 Q 0.0408 0.5267 0.4324 145 E 0.0380 0.3530 0.6091 146 T 0.0571 0.3884 0.5545 147 P 0.0460 0.4738 0.4802 148 K 0.0482 0.3416 0.6102 149 H 0.0567 0.2372 0.7061 150 L 0.0375 0.0576 0.9050