# This file is the result of combining several RDB files, specifically # T0266.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0266.t2k.stride-ebghtl.rdb (weight 1.24869) # T0266.t2k.str2.rdb (weight 1.54758) # T0266.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 T0266.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0266 # 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 T0266.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 252 # # ============================================ # Comments from T0266.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0266 # 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 T0266.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 252 # # ============================================ # Comments from T0266.t2k.str2.rdb # ============================================ # TARGET T0266 # 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 T0266.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 252 # # ============================================ # Comments from T0266.t2k.alpha.rdb # ============================================ # TARGET T0266 # 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 T0266.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 252 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0525 0.0679 0.8796 2 L 0.0707 0.2446 0.6847 3 E 0.0615 0.3057 0.6328 4 K 0.0324 0.7421 0.2255 5 V 0.0059 0.9234 0.0707 6 E 0.0055 0.9439 0.0507 7 E 0.0059 0.9494 0.0447 8 W 0.0047 0.9554 0.0398 9 I 0.0049 0.9508 0.0443 10 K 0.0051 0.9319 0.0629 11 A 0.0062 0.8813 0.1125 12 R 0.0442 0.3882 0.5676 13 G 0.0455 0.0222 0.9322 14 L 0.0787 0.0098 0.9115 15 T 0.2120 0.0251 0.7629 16 W 0.7694 0.0132 0.2174 17 R 0.8773 0.0065 0.1161 18 L 0.9049 0.0035 0.0915 19 L 0.8469 0.0067 0.1464 20 I 0.6744 0.0107 0.3150 21 M 0.3112 0.0175 0.6713 22 Q 0.1465 0.0309 0.8225 23 K 0.0830 0.0523 0.8647 24 P 0.0835 0.0460 0.8705 25 T 0.0346 0.2430 0.7224 26 R 0.0359 0.2514 0.7127 27 T 0.0835 0.2766 0.6399 28 V 0.0055 0.9274 0.0671 29 A 0.0051 0.9456 0.0493 30 E 0.0052 0.9539 0.0409 31 A 0.0049 0.9565 0.0386 32 A 0.0048 0.9546 0.0406 33 A 0.0052 0.9417 0.0531 34 L 0.0069 0.8898 0.1033 35 L 0.0467 0.4323 0.5210 36 G 0.0362 0.0333 0.9306 37 V 0.0531 0.0092 0.9377 38 S 0.0675 0.0105 0.9220 39 E 0.0118 0.7043 0.2839 40 S 0.0116 0.7441 0.2443 41 E 0.0282 0.7683 0.2034 42 I 0.2560 0.4191 0.3249 43 V 0.4727 0.1657 0.3616 44 K 0.6607 0.1125 0.2268 45 T 0.8107 0.0489 0.1404 46 L 0.8503 0.0352 0.1146 47 I 0.9079 0.0114 0.0807 48 V 0.8803 0.0081 0.1116 49 L 0.8465 0.0122 0.1413 50 D 0.6832 0.0219 0.2949 51 N 0.1614 0.0781 0.7605 52 A 0.0475 0.0559 0.8966 53 G 0.0545 0.0477 0.8978 54 G 0.3285 0.0156 0.6559 55 V 0.8386 0.0036 0.1579 56 Y 0.9220 0.0035 0.0744 57 A 0.9296 0.0033 0.0671 58 V 0.9267 0.0033 0.0700 59 V 0.9054 0.0050 0.0896 60 I 0.8137 0.0062 0.1801 61 P 0.4876 0.0198 0.4926 62 G 0.1079 0.1044 0.7877 63 D 0.0567 0.2004 0.7429 64 K 0.0824 0.2792 0.6384 65 R 0.2945 0.2086 0.4969 66 L 0.4130 0.0960 0.4910 67 N 0.2571 0.0633 0.6796 68 I 0.0051 0.9270 0.0678 69 N 0.0048 0.9478 0.0474 70 S 0.0049 0.9541 0.0410 71 M 0.0048 0.9534 0.0418 72 K 0.0051 0.9409 0.0540 73 E 0.0067 0.8875 0.1058 74 L 0.0134 0.8123 0.1743 75 A 0.0501 0.4795 0.4704 76 G 0.0303 0.0723 0.8975 77 K 0.0549 0.0965 0.8486 78 P 0.1810 0.0871 0.7319 79 V 0.3401 0.0489 0.6111 80 R 0.5474 0.0404 0.4121 81 L 0.5959 0.0280 0.3761 82 A 0.3214 0.0162 0.6624 83 R 0.1163 0.0167 0.8670 84 A 0.0051 0.9104 0.0844 85 N 0.0048 0.9293 0.0658 86 E 0.0051 0.9447 0.0502 87 V 0.0052 0.9532 0.0416 88 V 0.0064 0.9478 0.0458 89 E 0.0057 0.9322 0.0621 90 L 0.0079 0.9064 0.0857 91 T 0.0482 0.5899 0.3619 92 G 0.0423 0.0547 0.9030 93 Y 0.0832 0.0251 0.8918 94 P 0.1598 0.0385 0.8017 95 V 0.1431 0.1126 0.7443 96 G 0.1360 0.0847 0.7793 97 G 0.2149 0.0788 0.7063 98 V 0.2793 0.0597 0.6610 99 P 0.1755 0.0606 0.7638 100 P 0.1482 0.1438 0.7080 101 V 0.1304 0.1756 0.6940 102 A 0.1420 0.1349 0.7231 103 L 0.1653 0.1248 0.7100 104 P 0.1025 0.1437 0.7538 105 P 0.0855 0.1279 0.7866 106 N 0.0929 0.0737 0.8335 107 I 0.1711 0.0295 0.7994 108 V 0.4159 0.0378 0.5463 109 L 0.8555 0.0159 0.1287 110 V 0.8861 0.0098 0.1041 111 V 0.8037 0.0105 0.1858 112 D 0.3499 0.0373 0.6128 113 R 0.0321 0.4607 0.5072 114 I 0.0173 0.5547 0.4280 115 L 0.0201 0.6910 0.2889 116 L 0.0393 0.4952 0.4654 117 S 0.0646 0.2636 0.6718 118 R 0.1059 0.0680 0.8261 119 K 0.0719 0.1098 0.8183 120 K 0.4750 0.0762 0.4487 121 V 0.8364 0.0205 0.1431 122 Y 0.8876 0.0110 0.1013 123 G 0.8351 0.0157 0.1492 124 G 0.5729 0.0212 0.4059 125 G 0.1857 0.0984 0.7158 126 G 0.1094 0.0815 0.8091 127 R 0.1491 0.0742 0.7767 128 E 0.0712 0.0935 0.8353 129 N 0.0854 0.0636 0.8510 130 A 0.4618 0.0259 0.5122 131 L 0.7936 0.0099 0.1965 132 L 0.8660 0.0078 0.1262 133 E 0.8721 0.0060 0.1219 134 F 0.7305 0.0093 0.2602 135 S 0.3878 0.0144 0.5977 136 P 0.0105 0.8320 0.1576 137 R 0.0065 0.8742 0.1193 138 E 0.0074 0.8922 0.1004 139 L 0.0089 0.8995 0.0916 140 V 0.0102 0.8763 0.1136 141 E 0.0096 0.8145 0.1758 142 A 0.0175 0.6912 0.2913 143 T 0.0569 0.4079 0.5352 144 G 0.0556 0.1044 0.8400 145 A 0.1340 0.0534 0.8126 146 V 0.3775 0.1053 0.5172 147 V 0.6143 0.1285 0.2572 148 A 0.5652 0.1359 0.2989 149 D 0.5882 0.0941 0.3178 150 V 0.4450 0.1247 0.4303 151 S 0.2881 0.0833 0.6286 152 E 0.0539 0.0332 0.9128