# This file is the result of combining several RDB files, specifically # T0412.t04.dssp-ebghstl.rdb (weight 1.53986) # T0412.t04.stride-ebghtl.rdb (weight 1.24869) # T0412.t04.str2.rdb (weight 1.54758) # T0412.t04.alpha.rdb (weight 0.659012) # T0412.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0412.t2k.stride-ebghtl.rdb (weight 1.24869) # T0412.t2k.str2.rdb (weight 1.54758) # T0412.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 T0412.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0412 # Using neural net t04-2621-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 T0412.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 1764 # # ============================================ # Comments from T0412.t04.stride-ebghtl.rdb # ============================================ # TARGET T0412 # 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 T0412.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 1764 # # ============================================ # Comments from T0412.t04.str2.rdb # ============================================ # TARGET T0412 # 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 T0412.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 1764 # # ============================================ # Comments from T0412.t04.alpha.rdb # ============================================ # TARGET T0412 # 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 T0412.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 1764 # # ============================================ # Comments from T0412.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0412 # 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 T0412.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 365 # # ============================================ # Comments from T0412.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0412 # 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 T0412.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 365 # # ============================================ # Comments from T0412.t2k.str2.rdb # ============================================ # TARGET T0412 # 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 T0412.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 365 # # ============================================ # Comments from T0412.t2k.alpha.rdb # ============================================ # TARGET T0412 # 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 T0412.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 365 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0787 0.1230 0.7983 2 N 0.0503 0.2613 0.6884 3 A 0.0527 0.2200 0.7273 4 L 0.0636 0.1814 0.7550 5 F 0.0749 0.1961 0.7290 6 S 0.0123 0.8118 0.1760 7 S 0.0073 0.8744 0.1183 8 R 0.0069 0.8932 0.1000 9 D 0.0074 0.8756 0.1171 10 I 0.0101 0.8496 0.1403 11 L 0.0070 0.8899 0.1032 12 E 0.0049 0.9443 0.0508 13 V 0.0048 0.9549 0.0403 14 L 0.0048 0.9565 0.0387 15 Q 0.0047 0.9582 0.0371 16 D 0.0047 0.9577 0.0376 17 I 0.0047 0.9557 0.0396 18 H 0.0049 0.9500 0.0452 19 M 0.0055 0.9087 0.0858 20 E 0.0077 0.8343 0.1580 21 T 0.0468 0.4743 0.4789 22 G 0.0370 0.0413 0.9217 23 E 0.1365 0.0290 0.8345 24 T 0.5683 0.0195 0.4122 25 V 0.8012 0.0152 0.1836 26 A 0.8826 0.0118 0.1055 27 I 0.8819 0.0135 0.1046 28 A 0.8777 0.0127 0.1096 29 T 0.8689 0.0097 0.1214 30 K 0.7206 0.0345 0.2449 31 N 0.2906 0.0440 0.6654 32 D 0.0607 0.0648 0.8745 33 I 0.1767 0.0401 0.7832 34 Y 0.7942 0.0077 0.1981 35 L 0.9211 0.0032 0.0756 36 Q 0.9275 0.0033 0.0692 37 Y 0.9284 0.0033 0.0683 38 I 0.9206 0.0035 0.0759 39 Q 0.8850 0.0074 0.1076 40 I 0.8315 0.0085 0.1599 41 I 0.7545 0.0125 0.2330 42 E 0.5574 0.0299 0.4127 43 S 0.3013 0.0313 0.6674 44 V 0.1807 0.0671 0.7521 45 H 0.2080 0.0373 0.7547 46 A 0.4338 0.0315 0.5347 47 L 0.6820 0.0184 0.2996 48 R 0.7996 0.0155 0.1850 49 F 0.7946 0.0176 0.1878 50 H 0.7306 0.0165 0.2528 51 V 0.5629 0.0205 0.4166 52 D 0.3019 0.0293 0.6688 53 E 0.1079 0.0803 0.8118 54 N 0.0726 0.0516 0.8758 55 A 0.2411 0.0346 0.7243 56 I 0.5216 0.0266 0.4518 57 R 0.5022 0.0266 0.4712 58 P 0.4249 0.0512 0.5239 59 L 0.3863 0.1444 0.4693 60 T 0.3736 0.1785 0.4480 61 M 0.2857 0.2489 0.4654 62 S 0.1742 0.3052 0.5205 63 S 0.1009 0.5590 0.3401 64 N 0.0603 0.6850 0.2547 65 G 0.0768 0.7086 0.2146 66 W 0.0909 0.7844 0.1248 67 M 0.1237 0.7787 0.0976 68 L 0.1108 0.7875 0.1017 69 M 0.1009 0.7382 0.1610 70 S 0.0745 0.5261 0.3995 71 T 0.0678 0.2366 0.6956 72 M 0.0702 0.0306 0.8992 73 N 0.0559 0.0277 0.9164 74 D 0.0067 0.8883 0.1050 75 K 0.0051 0.9282 0.0668 76 A 0.0052 0.9453 0.0495 77 I 0.0048 0.9535 0.0418 78 D 0.0051 0.9519 0.0431 79 N 0.0048 0.9460 0.0492 80 T 0.0049 0.9385 0.0566 81 V 0.0062 0.9170 0.0769 82 R 0.0063 0.8133 0.1804 83 R 0.0125 0.6158 0.3716 84 A 0.0584 0.3104 0.6312 85 N 0.0589 0.1644 0.7767 86 T 0.0731 0.1944 0.7325 87 I 0.0733 0.2259 0.7007 88 T 0.0897 0.2278 0.6825 89 Q 0.0984 0.1495 0.7521 90 K 0.0815 0.0657 0.8528 91 D 0.0262 0.2560 0.7178 92 G 0.0343 0.1924 0.7733 93 I 0.1059 0.1580 0.7360 94 R 0.1574 0.1058 0.7368 95 F 0.1456 0.0823 0.7721 96 E 0.0953 0.0668 0.8379 97 V 0.0050 0.9400 0.0550 98 D 0.0048 0.9483 0.0469 99 D 0.0049 0.9519 0.0432 100 M 0.0047 0.9571 0.0382 101 M 0.0047 0.9573 0.0380 102 A 0.0047 0.9548 0.0405 103 R 0.0048 0.9538 0.0415 104 I 0.0047 0.9552 0.0400 105 R 0.0047 0.9544 0.0409 106 Q 0.0048 0.9494 0.0459 107 V 0.0052 0.9413 0.0535 108 R 0.0062 0.9259 0.0679 109 E 0.0076 0.8609 0.1315 110 Q 0.0435 0.5021 0.4544 111 G 0.0448 0.1170 0.8382 112 Y 0.1636 0.0947 0.7417 113 A 0.4416 0.0600 0.4984 114 S 0.4613 0.0591 0.4796 115 A 0.3494 0.0472 0.6035 116 E 0.0858 0.3814 0.5327 117 H 0.0708 0.3889 0.5403 118 I 0.1876 0.3202 0.4922 119 P 0.2247 0.1836 0.5916 120 F 0.2325 0.0988 0.6687 121 V 0.1369 0.1287 0.7344 122 G 0.1504 0.0660 0.7836 123 G 0.5422 0.0208 0.4370 124 G 0.7822 0.0249 0.1929 125 T 0.8872 0.0081 0.1048 126 I 0.8988 0.0063 0.0948 127 C 0.8907 0.0071 0.1022 128 V 0.8495 0.0063 0.1442 129 L 0.8343 0.0050 0.1607 130 L 0.7246 0.0125 0.2629 131 P 0.6641 0.0188 0.3171 132 M 0.2401 0.0237 0.7362 133 T 0.0313 0.1207 0.8480 134 I 0.0513 0.0367 0.9120 135 Q 0.0581 0.0343 0.9076 136 G 0.2683 0.0131 0.7186 137 Q 0.7666 0.0041 0.2292 138 P 0.8686 0.0097 0.1217 139 V 0.9192 0.0043 0.0765 140 T 0.9248 0.0038 0.0713 141 M 0.9201 0.0048 0.0751 142 G 0.9089 0.0049 0.0863 143 L 0.8237 0.0203 0.1560 144 G 0.6099 0.0368 0.3534 145 G 0.3120 0.0435 0.6445 146 A 0.2145 0.1388 0.6466 147 L 0.1403 0.3402 0.5194 148 D 0.1446 0.3397 0.5157 149 R 0.1382 0.2511 0.6106 150 I 0.1144 0.0945 0.7911 151 K 0.0664 0.0782 0.8554 152 Q 0.0067 0.8299 0.1634 153 N 0.0063 0.8447 0.1491 154 Y 0.0062 0.8841 0.1097 155 D 0.0069 0.9007 0.0923 156 R 0.0077 0.8928 0.0995 157 Y 0.0077 0.8744 0.1179 158 L 0.0067 0.8939 0.0993 159 E 0.0052 0.9407 0.0541 160 L 0.0048 0.9512 0.0440 161 L 0.0048 0.9550 0.0401 162 L 0.0048 0.9552 0.0400 163 N 0.0048 0.9534 0.0418 164 G 0.0049 0.9522 0.0429 165 V 0.0048 0.9511 0.0441 166 Q 0.0049 0.9482 0.0470 167 Q 0.0050 0.9405 0.0545 168 L 0.0051 0.9376 0.0573 169 K 0.0055 0.9342 0.0603 170 K 0.0056 0.9063 0.0881 171 S 0.0078 0.8614 0.1308 172 D 0.0187 0.7641 0.2172 173 S 0.0428 0.4124 0.5448 174 F 0.0346 0.1047 0.8606 175 H 0.0728 0.0931 0.8340 176 Q 0.1343 0.0671 0.7986 177 P 0.1247 0.0416 0.8338 178 I 0.0526 0.0346 0.9127