# This file is the result of combining several RDB files, specifically # T0425.t04.str2.rdb (weight 1.54425) # T0425.t04.str4.rdb (weight 0.924988) # T0425.t04.pb.rdb (weight 0.789901) # T0425.t04.bys.rdb (weight 0.748322) # T0425.t04.alpha.rdb (weight 0.678173) # 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 T0425.t04.str2.rdb # ============================================ # TARGET T0425 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0425.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 205.135 # # ============================================ # Comments from T0425.t04.str4.rdb # ============================================ # TARGET T0425 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0425.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 205.135 # # ============================================ # Comments from T0425.t04.pb.rdb # ============================================ # TARGET T0425 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0425.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 205.135 # # ============================================ # Comments from T0425.t04.bys.rdb # ============================================ # TARGET T0425 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0425.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 205.135 # # ============================================ # Comments from T0425.t04.alpha.rdb # ============================================ # TARGET T0425 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0425.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 205.135 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2338 0.0868 0.6794 2 S 0.2810 0.0551 0.6639 3 K 0.5501 0.0153 0.4346 4 I 0.7823 0.0068 0.2109 5 I 0.8063 0.0048 0.1889 6 C 0.8082 0.0050 0.1868 7 L 0.7886 0.0092 0.2022 8 T 0.6756 0.0095 0.3149 9 A 0.3515 0.1482 0.5003 10 G 0.1834 0.1162 0.7004 11 H 0.1618 0.1273 0.7109 12 S 0.1652 0.1466 0.6882 13 N 0.1818 0.1318 0.6865 14 T 0.2134 0.1449 0.6417 15 D 0.2290 0.0677 0.7033 16 P 0.1006 0.3361 0.5634 17 G 0.1193 0.2378 0.6429 18 A 0.2609 0.1844 0.5548 19 V 0.2969 0.1501 0.5530 20 N 0.2303 0.1189 0.6507 21 G 0.1373 0.1182 0.7445 22 S 0.1762 0.1311 0.6927 23 D 0.2126 0.2304 0.5570 24 R 0.1848 0.4046 0.4106 25 E 0.0819 0.6932 0.2249 26 A 0.0356 0.8200 0.1444 27 D 0.0342 0.8404 0.1255 28 L 0.0262 0.8734 0.1004 29 A 0.0108 0.9074 0.0818 30 Q 0.0084 0.9195 0.0722 31 D 0.0083 0.9233 0.0684 32 M 0.0083 0.9216 0.0701 33 R 0.0083 0.9233 0.0684 34 N 0.0083 0.9247 0.0670 35 I 0.0083 0.9245 0.0672 36 V 0.0083 0.9222 0.0694 37 A 0.0083 0.9233 0.0684 38 S 0.0083 0.9236 0.0681 39 I 0.0084 0.9191 0.0725 40 L 0.0087 0.9058 0.0855 41 R 0.0102 0.8568 0.1330 42 N 0.0158 0.7422 0.2420 43 D 0.0578 0.4613 0.4809 44 Y 0.0760 0.1595 0.7644 45 G 0.0851 0.0585 0.8564 46 L 0.3323 0.0125 0.6552 47 T 0.6033 0.0149 0.3818 48 V 0.7604 0.0061 0.2335 49 K 0.7524 0.0122 0.2354 50 T 0.7290 0.0073 0.2636 51 D 0.5736 0.0277 0.3987 52 G 0.3773 0.0531 0.5696 53 T 0.1889 0.1054 0.7057 54 G 0.1183 0.1113 0.7704 55 K 0.1424 0.1359 0.7217 56 G 0.2047 0.1287 0.6666 57 N 0.3099 0.0852 0.6049 58 M 0.3663 0.0650 0.5687 59 P 0.2403 0.0396 0.7200 60 L 0.0445 0.6124 0.3430 61 R 0.0189 0.7871 0.1939 62 D 0.0181 0.8458 0.1361 63 A 0.0220 0.8709 0.1071 64 V 0.0356 0.8604 0.1040 65 K 0.0287 0.8640 0.1073 66 L 0.0399 0.7870 0.1731 67 I 0.0872 0.5672 0.3456 68 R 0.0997 0.2479 0.6524 69 G 0.0539 0.1249 0.8212 70 S 0.1971 0.0524 0.7505 71 D 0.2871 0.0594 0.6535 72 V 0.6940 0.0290 0.2771 73 A 0.7275 0.0127 0.2598 74 I 0.8010 0.0069 0.1921 75 E 0.7914 0.0112 0.1975 76 F 0.7415 0.0303 0.2282 77 H 0.6090 0.0553 0.3357 78 T 0.3915 0.1460 0.4625 79 N 0.2305 0.1697 0.5997 80 A 0.1503 0.2907 0.5590 81 A 0.1663 0.2366 0.5972 82 A 0.1274 0.2629 0.6098 83 N 0.1417 0.1874 0.6710 84 K 0.1105 0.2864 0.6030 85 T 0.1800 0.1717 0.6483 86 A 0.2782 0.1236 0.5982 87 T 0.2873 0.0912 0.6214 88 G 0.4870 0.0425 0.4705 89 I 0.6862 0.0215 0.2923 90 E 0.7725 0.0146 0.2129 91 A 0.8042 0.0079 0.1879 92 L 0.7849 0.0116 0.2035 93 S 0.7224 0.0121 0.2655 94 T 0.4240 0.0212 0.5548 95 P 0.2004 0.1418 0.6578 96 K 0.0949 0.2801 0.6249 97 N 0.0981 0.2354 0.6665 98 K 0.0902 0.3945 0.5153 99 R 0.0595 0.5761 0.3644 100 W 0.0412 0.7129 0.2459 101 C 0.0196 0.8520 0.1284 102 Q 0.0097 0.9056 0.0847 103 V 0.0088 0.9151 0.0761 104 L 0.0086 0.9189 0.0725 105 G 0.0083 0.9213 0.0703 106 K 0.0083 0.9228 0.0690 107 A 0.0083 0.9227 0.0690 108 V 0.0084 0.9183 0.0733 109 A 0.0086 0.9103 0.0811 110 K 0.0093 0.8923 0.0985 111 K 0.0188 0.7595 0.2217 112 T 0.0668 0.4500 0.4832 113 G 0.0600 0.2815 0.6585 114 W 0.1355 0.2810 0.5836 115 K 0.2053 0.2062 0.5885 116 L 0.2362 0.1754 0.5884 117 R 0.2467 0.1385 0.6149 118 G 0.1693 0.1584 0.6723 119 E 0.1459 0.2624 0.5918 120 D 0.1228 0.1788 0.6984 121 G 0.1145 0.1062 0.7793 122 F 0.2596 0.0418 0.6986 123 K 0.2681 0.0287 0.7032 124 P 0.2165 0.1336 0.6498 125 D 0.1358 0.3211 0.5431 126 N 0.1306 0.2635 0.6059 127 A 0.1535 0.2452 0.6014 128 G 0.1701 0.2092 0.6207 129 Q 0.2161 0.1964 0.5875 130 H 0.4155 0.1297 0.4548 131 S 0.6106 0.0971 0.2923 132 R 0.7131 0.0633 0.2236 133 L 0.6605 0.0896 0.2499 134 A 0.5003 0.1734 0.3263 135 Y 0.3407 0.2102 0.4491 136 A 0.2270 0.2312 0.5418 137 Q 0.1987 0.1553 0.6460 138 A 0.2616 0.0964 0.6420 139 G 0.3081 0.1016 0.5903 140 G 0.5952 0.0608 0.3440 141 I 0.7396 0.0301 0.2303 142 V 0.7670 0.0212 0.2118 143 F 0.7448 0.0311 0.2241 144 E 0.6859 0.0336 0.2805 145 P 0.5334 0.1038 0.3628 146 F 0.4844 0.1116 0.4040 147 F 0.5146 0.1093 0.3761 148 I 0.3828 0.1138 0.5035 149 S 0.2397 0.0846 0.6757 150 N 0.1738 0.0512 0.7749 151 D 0.0214 0.6813 0.2973 152 T 0.0145 0.8038 0.1817 153 D 0.0158 0.8681 0.1160 154 L 0.0112 0.8924 0.0964 155 A 0.0108 0.8728 0.1164 156 L 0.0172 0.8075 0.1754 157 F 0.0296 0.7640 0.2063 158 K 0.0579 0.5197 0.4224 159 T 0.1067 0.3458 0.5475 160 T 0.0263 0.5233 0.4504 161 K 0.0219 0.6208 0.3572 162 W 0.0246 0.7294 0.2460 163 G 0.0224 0.7924 0.1852 164 I 0.0205 0.8605 0.1190 165 C 0.0111 0.9063 0.0827 166 R 0.0094 0.9182 0.0723 167 A 0.0094 0.9201 0.0705 168 I 0.0100 0.9156 0.0744 169 A 0.0150 0.8962 0.0888 170 D 0.0149 0.8624 0.1227 171 A 0.0462 0.8066 0.1471 172 I 0.1220 0.6846 0.1934 173 A 0.1523 0.5607 0.2870 174 M 0.1957 0.4616 0.3427 175 E 0.1905 0.3141 0.4954 176 L 0.1546 0.2072 0.6382 177 G 0.1298 0.0912 0.7790 178 A 0.1511 0.1920 0.6570 179 A 0.1739 0.1899 0.6362 180 K 0.2020 0.1725 0.6255 181 V 0.2267 0.1336 0.6397