# This file is the result of combining several RDB files, specifically # T0169.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0169.t2k.stride-ebghtl.rdb (weight 1.24869) # T0169.t2k.str.rdb (weight 1.53983) # T0169.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 T0169.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0169 # 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 T0169.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 246 # # ============================================ # Comments from T0169.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0169 # 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 T0169.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 246 # # ============================================ # Comments from T0169.t2k.str.rdb # ============================================ # TARGET T0169 # 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 T0169.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 246 # # ============================================ # Comments from T0169.t2k.alpha.rdb # ============================================ # TARGET T0169 # 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 T0169.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 246 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1181 0.0081 0.8738 2 D 0.5015 0.0088 0.4897 3 I 0.6158 0.0109 0.3733 4 R 0.5362 0.0166 0.4473 5 T 0.4321 0.0156 0.5523 6 I 0.1864 0.0147 0.7989 7 T 0.0981 0.0151 0.8868 8 S 0.0091 0.6367 0.3542 9 S 0.0074 0.6402 0.3524 10 D 0.0176 0.6793 0.3031 11 Y 0.0061 0.8972 0.0967 12 E 0.0046 0.9247 0.0707 13 M 0.0047 0.9328 0.0624 14 V 0.0049 0.9479 0.0472 15 T 0.0053 0.9508 0.0439 16 S 0.0050 0.9417 0.0533 17 V 0.0055 0.9302 0.0644 18 L 0.0056 0.9138 0.0807 19 N 0.0066 0.8339 0.1595 20 E 0.0136 0.7121 0.2743 21 W 0.0349 0.4809 0.4842 22 W 0.0503 0.2023 0.7475 23 G 0.0409 0.2190 0.7401 24 G 0.0391 0.2699 0.6910 25 R 0.0437 0.3415 0.6148 26 Q 0.0402 0.4700 0.4897 27 L 0.0367 0.5212 0.4421 28 K 0.0244 0.6665 0.3091 29 E 0.0113 0.8313 0.1574 30 K 0.0101 0.8710 0.1189 31 L 0.0120 0.8930 0.0950 32 P 0.0125 0.9114 0.0761 33 R 0.0125 0.9183 0.0692 34 L 0.0104 0.9139 0.0757 35 F 0.0116 0.8974 0.0910 36 F 0.0167 0.8425 0.1408 37 E 0.0245 0.6599 0.3155 38 H 0.0581 0.3057 0.6362 39 F 0.0543 0.1437 0.8020 40 Q 0.0402 0.1396 0.8201 41 D 0.1120 0.0802 0.8078 42 T 0.4587 0.0215 0.5198 43 S 0.8529 0.0063 0.1409 44 F 0.9207 0.0036 0.0757 45 I 0.9220 0.0038 0.0742 46 T 0.9105 0.0046 0.0849 47 S 0.8416 0.0103 0.1481 48 E 0.5906 0.0663 0.3431 49 H 0.0570 0.0203 0.9228 50 N 0.0456 0.0372 0.9171 51 S 0.7714 0.0074 0.2212 52 M 0.9119 0.0034 0.0847 53 T 0.8819 0.0161 0.1020 54 G 0.9188 0.0050 0.0762 55 F 0.9280 0.0037 0.0683 56 L 0.9252 0.0041 0.0707 57 I 0.9197 0.0048 0.0755 58 G 0.8822 0.0093 0.1085 59 F 0.8049 0.0114 0.1837 60 Q 0.5780 0.0321 0.3898 61 S 0.2394 0.0616 0.6990 62 Q 0.1294 0.1034 0.7672 63 S 0.1142 0.1106 0.7752 64 D 0.1479 0.1111 0.7410 65 P 0.1565 0.1238 0.7197 66 E 0.2994 0.0989 0.6016 67 T 0.7017 0.0352 0.2631 68 A 0.8359 0.0138 0.1503 69 Y 0.8833 0.0119 0.1047 70 I 0.8967 0.0163 0.0870 71 H 0.8429 0.0282 0.1289 72 F 0.8768 0.0178 0.1053 73 S 0.8723 0.0159 0.1118 74 G 0.8872 0.0097 0.1032 75 V 0.7709 0.0144 0.2147 76 H 0.3018 0.0178 0.6804 77 P 0.0078 0.6066 0.3856 78 D 0.0076 0.6152 0.3773 79 F 0.0128 0.7227 0.2645 80 R 0.0233 0.4314 0.5453 81 K 0.0295 0.2647 0.7057 82 M 0.0621 0.2334 0.7045 83 Q 0.0565 0.2681 0.6754 84 I 0.0338 0.6458 0.3204 85 G 0.0074 0.8708 0.1218 86 K 0.0047 0.9509 0.0443 87 Q 0.0046 0.9560 0.0394 88 L 0.0044 0.9574 0.0382 89 Y 0.0044 0.9598 0.0358 90 D 0.0045 0.9589 0.0366 91 V 0.0044 0.9585 0.0371 92 F 0.0044 0.9578 0.0378 93 I 0.0044 0.9580 0.0375 94 E 0.0045 0.9567 0.0389 95 T 0.0046 0.9548 0.0406 96 V 0.0050 0.9513 0.0437 97 K 0.0050 0.9370 0.0580 98 Q 0.0096 0.8326 0.1578 99 R 0.0418 0.2333 0.7249 100 G 0.0363 0.0175 0.9462 101 C 0.1092 0.0087 0.8822 102 T 0.4049 0.0227 0.5724 103 R 0.8949 0.0040 0.1011 104 V 0.9189 0.0040 0.0771 105 K 0.9246 0.0038 0.0716 106 C 0.8927 0.0047 0.1026 107 V 0.8132 0.0066 0.1802 108 T 0.6065 0.0119 0.3816 109 S 0.2515 0.0235 0.7250 110 P 0.0713 0.1140 0.8147 111 V 0.0310 0.1486 0.8205 112 N 0.0366 0.2555 0.7079 113 K 0.0116 0.8327 0.1557 114 V 0.0072 0.9191 0.0737 115 S 0.0050 0.9481 0.0470 116 I 0.0044 0.9575 0.0381 117 A 0.0047 0.9575 0.0378 118 Y 0.0046 0.9573 0.0381 119 H 0.0052 0.9499 0.0449 120 T 0.0070 0.9282 0.0648 121 K 0.0075 0.8282 0.1643 122 L 0.0426 0.3853 0.5721 123 G 0.0574 0.0271 0.9155 124 F 0.2140 0.0159 0.7701 125 D 0.6476 0.0189 0.3335 126 I 0.7707 0.0199 0.2095 127 E 0.7474 0.0429 0.2097 128 K 0.7284 0.0310 0.2406 129 G 0.7642 0.0323 0.2035 130 T 0.7703 0.0239 0.2059 131 K 0.6784 0.0516 0.2700 132 T 0.4365 0.0543 0.5093 133 V 0.2117 0.1076 0.6807 134 N 0.1265 0.0920 0.7815 135 G 0.2239 0.0855 0.6906 136 I 0.4133 0.0930 0.4937 137 S 0.6438 0.0625 0.2937 138 V 0.7068 0.0628 0.2304 139 F 0.6930 0.0689 0.2381 140 A 0.6425 0.0686 0.2889 141 N 0.5334 0.0661 0.4004 142 Y 0.3303 0.0952 0.5745 143 D 0.1281 0.0732 0.7987 144 G 0.0784 0.0534 0.8683 145 P 0.0866 0.0856 0.8278 146 G 0.1408 0.1973 0.6619 147 Q 0.1911 0.2816 0.5273 148 D 0.2730 0.3176 0.4094 149 R 0.3637 0.4505 0.1858 150 V 0.4749 0.3854 0.1398 151 L 0.4954 0.3774 0.1272 152 F 0.4816 0.3415 0.1769 153 V 0.4441 0.3039 0.2519 154 K 0.3202 0.2453 0.4344 155 N 0.1623 0.1186 0.7192 156 I 0.0457 0.0383 0.9160