# This file is the result of combining several RDB files, specifically # T0317.t04.dssp-ebghstl.rdb (weight 1.53986) # T0317.t04.stride-ebghtl.rdb (weight 1.24869) # T0317.t04.str2.rdb (weight 1.54758) # T0317.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 T0317.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0317 # 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 T0317.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 1621 # # ============================================ # Comments from T0317.t04.stride-ebghtl.rdb # ============================================ # TARGET T0317 # 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 T0317.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 1621 # # ============================================ # Comments from T0317.t04.str2.rdb # ============================================ # TARGET T0317 # Using neural net t06-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 T0317.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 1621 # # ============================================ # Comments from T0317.t04.alpha.rdb # ============================================ # TARGET T0317 # 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 T0317.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 1621 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0770 0.0526 0.8704 2 G 0.1021 0.0496 0.8483 3 T 0.1809 0.0800 0.7391 4 S 0.2457 0.1236 0.6306 5 E 0.2448 0.1419 0.6133 6 A 0.1952 0.0755 0.7293 7 A 0.1220 0.0383 0.8397 8 P 0.0926 0.0257 0.8817 9 P 0.0803 0.0361 0.8835 10 P 0.1068 0.0583 0.8349 11 F 0.0979 0.2654 0.6367 12 A 0.1196 0.3504 0.5300 13 R 0.2134 0.3180 0.4686 14 V 0.3065 0.1524 0.5411 15 A 0.1792 0.0679 0.7529 16 P 0.0830 0.2174 0.6996 17 A 0.1894 0.1789 0.6317 18 L 0.5381 0.1096 0.3523 19 F 0.6810 0.0608 0.2582 20 I 0.5748 0.0824 0.3427 21 G 0.2598 0.0607 0.6795 22 N 0.1895 0.0814 0.7291 23 A 0.2019 0.2205 0.5776 24 R 0.2109 0.3275 0.4616 25 A 0.1720 0.4180 0.4099 26 A 0.1085 0.4810 0.4105 27 G 0.0814 0.4068 0.5118 28 A 0.0998 0.4665 0.4337 29 T 0.0266 0.8200 0.1534 30 E 0.0100 0.9198 0.0702 31 L 0.0082 0.9431 0.0487 32 L 0.0078 0.9460 0.0462 33 V 0.0074 0.9395 0.0531 34 R 0.0096 0.8873 0.1031 35 A 0.0425 0.3565 0.6010 36 G 0.0529 0.0154 0.9318 37 I 0.2017 0.0071 0.7912 38 T 0.6046 0.0247 0.3707 39 L 0.9232 0.0034 0.0734 40 C 0.9314 0.0031 0.0655 41 V 0.9292 0.0034 0.0674 42 N 0.8987 0.0035 0.0978 43 V 0.6285 0.0132 0.3583 44 S 0.3301 0.0244 0.6455 45 R 0.1595 0.0642 0.7763 46 Q 0.1203 0.0518 0.8279 47 Q 0.1012 0.0298 0.8690 48 P 0.0703 0.0567 0.8730 49 G 0.0794 0.0403 0.8803 50 P 0.0977 0.0757 0.8267 51 R 0.1393 0.0843 0.7764 52 A 0.1560 0.0571 0.7869 53 P 0.0895 0.0964 0.8141 54 G 0.2094 0.0569 0.7337 55 V 0.6208 0.0154 0.3637 56 A 0.7813 0.0134 0.2053 57 E 0.8981 0.0055 0.0964 58 L 0.8658 0.0072 0.1270 59 R 0.8054 0.0062 0.1883 60 V 0.5925 0.0072 0.4003 61 P 0.3868 0.0101 0.6031 62 V 0.2279 0.0498 0.7223 63 F 0.1349 0.0676 0.7975 64 D 0.1017 0.0647 0.8336 65 D 0.0611 0.0814 0.8576 66 P 0.0438 0.1542 0.8020 67 A 0.0575 0.2784 0.6640 68 E 0.0350 0.4807 0.4843 69 D 0.0423 0.5022 0.4556 70 L 0.0311 0.6508 0.3182 71 L 0.0196 0.7134 0.2669 72 T 0.0170 0.7027 0.2803 73 H 0.0169 0.7002 0.2829 74 L 0.0078 0.8709 0.1213 75 E 0.0051 0.9417 0.0532 76 P 0.0048 0.9508 0.0445 77 T 0.0047 0.9574 0.0379 78 C 0.0047 0.9593 0.0360 79 A 0.0046 0.9606 0.0348 80 A 0.0047 0.9581 0.0372 81 M 0.0047 0.9563 0.0390 82 E 0.0048 0.9503 0.0450 83 A 0.0051 0.9340 0.0609 84 A 0.0079 0.9134 0.0787 85 V 0.0209 0.8463 0.1328 86 R 0.0230 0.6921 0.2850 87 D 0.0380 0.2500 0.7120 88 G 0.0372 0.0335 0.9293 89 G 0.0723 0.0123 0.9155 90 S 0.4846 0.0058 0.5096 91 C 0.9113 0.0037 0.0851 92 L 0.9303 0.0033 0.0664 93 V 0.9289 0.0033 0.0678 94 Y 0.8635 0.0050 0.1315 95 C 0.4688 0.0198 0.5114 96 K 0.1386 0.0877 0.7736 97 N 0.0928 0.0975 0.8097 98 G 0.0724 0.1168 0.8107 99 R 0.1418 0.1818 0.6764 100 S 0.1613 0.2714 0.5674 101 R 0.0633 0.5959 0.3408 102 S 0.0400 0.8030 0.1570 103 A 0.0128 0.9329 0.0542 104 A 0.0077 0.9532 0.0391 105 V 0.0053 0.9591 0.0356 106 C 0.0048 0.9603 0.0349 107 T 0.0047 0.9606 0.0347 108 A 0.0047 0.9607 0.0347 109 Y 0.0047 0.9599 0.0353 110 L 0.0048 0.9582 0.0371 111 M 0.0051 0.9526 0.0423 112 R 0.0056 0.9408 0.0535 113 H 0.0093 0.8776 0.1132 114 R 0.0425 0.3336 0.6239 115 G 0.0340 0.0258 0.9402 116 H 0.0782 0.0109 0.9109 117 S 0.1000 0.0110 0.8890 118 L 0.0049 0.9429 0.0522 119 D 0.0046 0.9608 0.0346 120 R 0.0047 0.9606 0.0347 121 A 0.0047 0.9610 0.0344 122 F 0.0047 0.9602 0.0351 123 Q 0.0046 0.9603 0.0351 124 M 0.0047 0.9583 0.0370 125 V 0.0048 0.9521 0.0430 126 K 0.0054 0.9364 0.0581 127 S 0.0083 0.8420 0.1497 128 A 0.0261 0.6265 0.3474 129 R 0.0718 0.0769 0.8513 130 P 0.0370 0.1711 0.7919 131 V 0.0707 0.1602 0.7691 132 A 0.1766 0.1025 0.7209 133 E 0.1989 0.0411 0.7600 134 P 0.1285 0.0366 0.8349 135 N 0.0656 0.0445 0.8899 136 L 0.0056 0.9012 0.0932 137 G 0.0051 0.9265 0.0684 138 F 0.0049 0.9496 0.0455 139 W 0.0047 0.9603 0.0351 140 A 0.0046 0.9611 0.0342 141 Q 0.0047 0.9600 0.0353 142 L 0.0047 0.9607 0.0347 143 Q 0.0046 0.9604 0.0350 144 K 0.0047 0.9583 0.0370 145 Y 0.0047 0.9562 0.0391 146 E 0.0047 0.9575 0.0378 147 Q 0.0047 0.9547 0.0406 148 T 0.0048 0.9502 0.0450 149 L 0.0053 0.9342 0.0605 150 Q 0.0070 0.8891 0.1039 151 A 0.0100 0.8085 0.1815 152 Q 0.0293 0.6340 0.3367 153 A 0.0482 0.3829 0.5689 154 I 0.0979 0.1693 0.7328 155 L 0.1083 0.0509 0.8407 156 P 0.0941 0.0466 0.8593 157 R 0.0819 0.0706 0.8475 158 E 0.0936 0.0581 0.8483 159 P 0.0825 0.0783 0.8392 160 I 0.0927 0.0492 0.8581 161 D 0.0848 0.0225 0.8928 162 P 0.0277 0.0977 0.8745 163 E 0.0242 0.0751 0.9007