# This file is the result of combining several RDB files, specifically # T0318.t04.dssp-ebghstl.rdb (weight 1.53986) # T0318.t04.stride-ebghtl.rdb (weight 1.24869) # T0318.t04.str2.rdb (weight 1.54758) # T0318.t04.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 T0318.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0318 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0318.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 2 # # ============================================ # Comments from T0318.t04.stride-ebghtl.rdb # ============================================ # TARGET T0318 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0318.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 2 # # ============================================ # Comments from T0318.t04.str2.rdb # ============================================ # TARGET T0318 # Using neural net t04-2621-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 T0318.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 2 # # ============================================ # Comments from T0318.t04.alpha.rdb # ============================================ # TARGET T0318 # Using neural net t04-2621-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 T0318.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1600 0.1870 0.6530 2 T 0.4226 0.1667 0.4106 3 Q 0.6736 0.1471 0.1792 4 V 0.7631 0.1359 0.1010 5 L 0.7727 0.1459 0.0815 6 V 0.7263 0.1660 0.1077 7 R 0.5458 0.2418 0.2124 8 N 0.1971 0.2375 0.5654 9 G 0.1674 0.2251 0.6075 10 I 0.4203 0.2687 0.3110 11 Q 0.4840 0.3006 0.2154 12 A 0.4682 0.3017 0.2302 13 V 0.3054 0.2986 0.3960 14 G 0.1509 0.1512 0.6979 15 D 0.0773 0.1539 0.7688 16 G 0.1204 0.1115 0.7681 17 L 0.3384 0.0387 0.6229 18 T 0.4863 0.0387 0.4750 19 S 0.8192 0.0151 0.1657 20 L 0.9077 0.0084 0.0839 21 I 0.9175 0.0094 0.0730 22 I 0.8960 0.0119 0.0921 23 V 0.6508 0.0433 0.3059 24 G 0.3384 0.0305 0.6310 25 K 0.3100 0.1375 0.5525 26 K 0.2901 0.3054 0.4045 27 S 0.3846 0.2707 0.3447 28 V 0.4405 0.3011 0.2584 29 L 0.4721 0.2776 0.2503 30 K 0.3783 0.3142 0.3075 31 N 0.4253 0.2246 0.3500 32 V 0.5808 0.1018 0.3174 33 T 0.5604 0.0900 0.3496 34 F 0.4808 0.1322 0.3870 35 E 0.2503 0.2034 0.5463 36 G 0.1501 0.1991 0.6508 37 K 0.1727 0.3909 0.4365 38 F 0.1108 0.7391 0.1501 39 K 0.0563 0.8655 0.0781 40 E 0.0901 0.8397 0.0702 41 V 0.0870 0.8359 0.0771 42 A 0.1168 0.7894 0.0938 43 Q 0.1036 0.7889 0.1074 44 K 0.0912 0.7681 0.1407 45 F 0.1437 0.6463 0.2100 46 V 0.2172 0.3749 0.4080 47 T 0.1548 0.2184 0.6268 48 D 0.0930 0.1036 0.8035 49 G 0.0290 0.1597 0.8114 50 D 0.0541 0.1712 0.7748 51 S 0.1077 0.3184 0.5739 52 W 0.0707 0.6425 0.2868 53 N 0.0808 0.6566 0.2626 54 S 0.1189 0.6469 0.2342 55 M 0.1311 0.6562 0.2127 56 I 0.1892 0.5812 0.2297 57 S 0.1730 0.4918 0.3352 58 R 0.1739 0.3568 0.4693 59 I 0.1620 0.0657 0.7723 60 P 0.1305 0.0777 0.7919 61 A 0.0655 0.2279 0.7066 62 S 0.0499 0.1793 0.7708 63 G 0.0431 0.1031 0.8538 64 R 0.0940 0.0771 0.8290 65 H 0.1081 0.0712 0.8207 66 P 0.1003 0.3498 0.5499 67 L 0.1156 0.5445 0.3399 68 H 0.1823 0.6078 0.2099 69 Y 0.1998 0.6667 0.1335 70 E 0.2625 0.6019 0.1356 71 L 0.2356 0.6173 0.1471 72 A 0.2123 0.6085 0.1793 73 H 0.2294 0.5683 0.2023 74 L 0.3182 0.4745 0.2073 75 I 0.4049 0.3245 0.2706 76 T 0.4022 0.2042 0.3937 77 V 0.2236 0.0428 0.7336 78 P 0.1501 0.0525 0.7974 79 D 0.1346 0.0938 0.7717 80 A 0.0764 0.2873 0.6363 81 S 0.0688 0.2723 0.6589 82 S 0.0918 0.2041 0.7041 83 R 0.0844 0.0965 0.8191 84 G 0.0904 0.0494 0.8603 85 N 0.1136 0.0472 0.8392 86 T 0.1109 0.0285 0.8605 87 P 0.1108 0.0627 0.8265 88 T 0.1019 0.1482 0.7499 89 N 0.0686 0.2520 0.6793 90 A 0.0337 0.6535 0.3128 91 H 0.0351 0.7308 0.2340 92 S 0.0643 0.7233 0.2124 93 I 0.0845 0.7395 0.1761 94 Y 0.0765 0.7370 0.1865 95 K 0.0695 0.7371 0.1934 96 E 0.0705 0.6347 0.2948 97 L 0.1421 0.4076 0.4502 98 K 0.1238 0.1000 0.7762 99 P 0.1583 0.0682 0.7735 100 I 0.1768 0.0455 0.7777 101 N 0.1748 0.0402 0.7850 102 Y 0.1098 0.0251 0.8651 103 P 0.0763 0.1436 0.7800 104 E 0.0508 0.2370 0.7122 105 D 0.0709 0.1951 0.7339 106 T 0.1504 0.1746 0.6749 107 K 0.2010 0.1649 0.6341 108 N 0.3303 0.0765 0.5932 109 V 0.5718 0.0214 0.4069 110 H 0.8176 0.0156 0.1668 111 F 0.9146 0.0104 0.0750 112 V 0.9040 0.0183 0.0776 113 L 0.8782 0.0257 0.0961 114 F 0.7558 0.0570 0.1872 115 A 0.4540 0.1110 0.4350 116 E 0.2277 0.1415 0.6308 117 Y 0.1137 0.2032 0.6831 118 P 0.0168 0.6815 0.3017 119 D 0.0157 0.7860 0.1983 120 V 0.0076 0.9123 0.0800 121 L 0.0063 0.9329 0.0608 122 S 0.0050 0.9424 0.0526 123 H 0.0047 0.9514 0.0439 124 V 0.0047 0.9592 0.0361 125 A 0.0047 0.9593 0.0360 126 A 0.0047 0.9582 0.0371 127 I 0.0051 0.9508 0.0441 128 A 0.0059 0.9354 0.0587 129 R 0.0096 0.8973 0.0932 130 T 0.0196 0.8235 0.1569 131 F 0.0452 0.7267 0.2280 132 C 0.1036 0.5168 0.3796 133 K 0.1184 0.4815 0.4002 134 F 0.1751 0.3933 0.4317 135 S 0.2075 0.3119 0.4806 136 M 0.2114 0.2513 0.5372 137 K 0.2394 0.2086 0.5520 138 T 0.2068 0.1804 0.6128 139 S 0.1454 0.1540 0.7006 140 G 0.1938 0.1301 0.6761 141 I 0.3746 0.1265 0.4989 142 R 0.4461 0.1280 0.4260 143 E 0.5698 0.1223 0.3078 144 L 0.5709 0.1195 0.3096 145 N 0.5498 0.0526 0.3976 146 V 0.6742 0.0281 0.2977 147 N 0.6332 0.0363 0.3305 148 I 0.6191 0.0559 0.3249 149 D 0.6552 0.1000 0.2448 150 V 0.7551 0.1036 0.1412 151 V 0.6258 0.1700 0.2043 152 C 0.4335 0.2218 0.3447 153 D 0.2166 0.2295 0.5539 154 K 0.1439 0.2636 0.5925 155 L 0.1722 0.1853 0.6425 156 T 0.1058 0.1407 0.7535 157 N 0.0518 0.2125 0.7357 158 E 0.0300 0.4099 0.5601 159 D 0.0765 0.3620 0.5615 160 A 0.1988 0.3873 0.4139 161 V 0.3795 0.3655 0.2550 162 F 0.4763 0.3345 0.1891 163 L 0.4114 0.3204 0.2683 164 T 0.2581 0.2995 0.4425 165 D 0.1826 0.2260 0.5915 166 L 0.0719 0.3474 0.5807 167 S 0.0539 0.4204 0.5258 168 E 0.0339 0.6276 0.3385 169 S 0.0531 0.6770 0.2699 170 V 0.0426 0.8370 0.1204 171 R 0.0400 0.8629 0.0971 172 E 0.0631 0.8361 0.1008 173 T 0.0600 0.8065 0.1335 174 A 0.0954 0.7206 0.1840 175 R 0.1312 0.6005 0.2684 176 L 0.1498 0.4244 0.4257 177 I 0.0837 0.1437 0.7726