# This file is the result of combining several RDB files, specifically # T0618.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0618.t2k.stride-ebghtl.rdb (weight 1.24869) # T0618.t2k.str2.rdb (weight 1.54758) # T0618.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 T0618.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0618 # 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 T0618.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 36 # # ============================================ # Comments from T0618.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0618 # 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 T0618.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 36 # # ============================================ # Comments from T0618.t2k.str2.rdb # ============================================ # TARGET T0618 # 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 T0618.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 36 # # ============================================ # Comments from T0618.t2k.alpha.rdb # ============================================ # TARGET T0618 # 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 T0618.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 36 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0524 0.0739 0.8737 2 K 0.0735 0.2550 0.6715 3 K 0.0519 0.4712 0.4770 4 E 0.0452 0.5501 0.4047 5 S 0.0406 0.5862 0.3732 6 Q 0.0380 0.6581 0.3039 7 V 0.0385 0.7014 0.2601 8 I 0.0418 0.6455 0.3128 9 F 0.0415 0.5952 0.3632 10 D 0.0305 0.6997 0.2698 11 K 0.0061 0.8902 0.1036 12 N 0.0063 0.9084 0.0853 13 V 0.0051 0.9503 0.0447 14 I 0.0047 0.9584 0.0369 15 E 0.0047 0.9592 0.0361 16 F 0.0049 0.9586 0.0365 17 V 0.0047 0.9606 0.0348 18 T 0.0047 0.9603 0.0350 19 V 0.0047 0.9600 0.0353 20 A 0.0047 0.9588 0.0365 21 A 0.0048 0.9573 0.0379 22 E 0.0049 0.9526 0.0425 23 F 0.0052 0.9405 0.0543 24 C 0.0070 0.9104 0.0826 25 A 0.0076 0.8288 0.1636 26 F 0.0134 0.7212 0.2654 27 L 0.0352 0.6148 0.3500 28 E 0.0414 0.4807 0.4779 29 R 0.0330 0.4523 0.5147 30 A 0.0214 0.5555 0.4232 31 E 0.0146 0.4778 0.5076 32 S 0.0204 0.4164 0.5632 33 M 0.0603 0.2578 0.6819 34 K 0.0510 0.2639 0.6851 35 R 0.0124 0.7740 0.2136 36 S 0.0071 0.8589 0.1340 37 T 0.0066 0.8783 0.1151 38 F 0.0053 0.9252 0.0695 39 V 0.0048 0.9468 0.0484 40 D 0.0049 0.9492 0.0459 41 T 0.0049 0.9526 0.0425 42 T 0.0049 0.9506 0.0445 43 L 0.0050 0.9458 0.0492 44 K 0.0054 0.9174 0.0772 45 I 0.0082 0.8728 0.1191 46 L 0.0085 0.8874 0.1041 47 P 0.0054 0.9053 0.0893 48 L 0.0053 0.9102 0.0845 49 L 0.0080 0.8699 0.1221 50 Y 0.0160 0.7854 0.1985 51 L 0.0308 0.7374 0.2318 52 K 0.0476 0.6947 0.2576 53 A 0.0758 0.5899 0.3342 54 S 0.0816 0.3991 0.5193 55 M 0.1023 0.2719 0.6259 56 L 0.1128 0.0802 0.8070 57 P 0.0881 0.0735 0.8384 58 K 0.0734 0.2630 0.6637 59 C 0.0934 0.2632 0.6433 60 E 0.1208 0.2025 0.6766 61 M 0.1285 0.1620 0.7095 62 I 0.1106 0.1749 0.7145 63 G 0.0676 0.2387 0.6937 64 D 0.0733 0.2101 0.7166 65 E 0.0922 0.1435 0.7643 66 S 0.0827 0.0692 0.8480 67 P 0.0918 0.1337 0.7745 68 E 0.1413 0.1273 0.7313 69 T 0.1354 0.1191 0.7455 70 Y 0.1853 0.0677 0.7470 71 V 0.1521 0.0516 0.7963 72 T 0.0756 0.0480 0.8763 73 E 0.0085 0.8682 0.1233 74 E 0.0062 0.9022 0.0917 75 I 0.0059 0.9274 0.0667 76 Y 0.0050 0.9453 0.0496 77 E 0.0048 0.9482 0.0469 78 V 0.0048 0.9475 0.0477 79 L 0.0048 0.9481 0.0471 80 R 0.0048 0.9504 0.0448 81 I 0.0052 0.9479 0.0469 82 N 0.0048 0.9455 0.0497 83 L 0.0051 0.9400 0.0549 84 A 0.0051 0.9271 0.0679 85 S 0.0060 0.8950 0.0989 86 I 0.0099 0.8105 0.1796 87 L 0.0458 0.4831 0.4711 88 A 0.0367 0.1195 0.8439 89 E 0.0519 0.2134 0.7347 90 K 0.0910 0.2787 0.6303 91 D 0.1436 0.2198 0.6366 92 D 0.1784 0.4000 0.4216 93 Y 0.2269 0.4685 0.3045 94 L 0.2336 0.5066 0.2599 95 E 0.2880 0.4368 0.2752 96 V 0.3024 0.3003 0.3973 97 F 0.2947 0.1365 0.5688 98 L 0.1387 0.0577 0.8037 99 P 0.0323 0.4340 0.5337 100 D 0.0331 0.4354 0.5315 101 M 0.0808 0.4400 0.4791 102 A 0.1303 0.2532 0.6165 103 Y 0.1200 0.1371 0.7429 104 S 0.0871 0.0768 0.8362 105 D 0.0638 0.0737 0.8625 106 E 0.1418 0.0385 0.8197 107 P 0.2378 0.0406 0.7216 108 I 0.3109 0.0508 0.6383 109 K 0.2861 0.1207 0.5931 110 K 0.1858 0.1477 0.6664 111 N 0.2052 0.1455 0.6493 112 I 0.0917 0.5449 0.3634 113 S 0.0450 0.6125 0.3425 114 E 0.0254 0.6214 0.3532 115 D 0.0269 0.6574 0.3156 116 L 0.0051 0.9417 0.0532 117 A 0.0050 0.9540 0.0410 118 D 0.0048 0.9519 0.0432 119 I 0.0048 0.9565 0.0388 120 Y 0.0048 0.9521 0.0430 121 Q 0.0049 0.9414 0.0537 122 D 0.0057 0.9217 0.0726 123 I 0.0066 0.9304 0.0631 124 K 0.0055 0.9264 0.0681 125 D 0.0064 0.8661 0.1275 126 F 0.0076 0.8785 0.1139 127 I 0.0169 0.8839 0.0992 128 F 0.0325 0.8652 0.1022 129 V 0.0484 0.8398 0.1118 130 F 0.0829 0.7813 0.1358 131 Q 0.0682 0.6933 0.2385 132 L 0.0343 0.4794 0.4863 133 G 0.0373 0.1907 0.7720 134 L 0.0390 0.3055 0.6555 135 N 0.0228 0.5169 0.4603 136 E 0.0240 0.6289 0.3472 137 T 0.0253 0.7037 0.2710 138 M 0.0086 0.8973 0.0941 139 N 0.0058 0.9427 0.0515 140 D 0.0050 0.9529 0.0421 141 S 0.0050 0.9564 0.0385 142 L 0.0047 0.9588 0.0365 143 A 0.0047 0.9583 0.0369 144 I 0.0047 0.9561 0.0392 145 C 0.0047 0.9536 0.0416 146 Q 0.0049 0.9468 0.0484 147 E 0.0058 0.9186 0.0755 148 N 0.0074 0.8398 0.1529 149 F 0.0112 0.7588 0.2300 150 G 0.0122 0.7363 0.2515 151 L 0.0121 0.7457 0.2422 152 L 0.0204 0.7297 0.2499 153 W 0.0109 0.8269 0.1622 154 G 0.0053 0.9299 0.0648 155 Q 0.0048 0.9541 0.0411 156 K 0.0048 0.9551 0.0402 157 L 0.0047 0.9591 0.0362 158 V 0.0047 0.9592 0.0361 159 N 0.0048 0.9577 0.0376 160 T 0.0047 0.9575 0.0377 161 M 0.0047 0.9577 0.0375 162 R 0.0047 0.9552 0.0401 163 A 0.0047 0.9527 0.0426 164 L 0.0048 0.9499 0.0453 165 H 0.0048 0.9418 0.0534 166 D 0.0051 0.9153 0.0796 167 V 0.0071 0.8899 0.1029 168 K 0.0149 0.8232 0.1619 169 Y 0.0231 0.7156 0.2613 170 S 0.0459 0.5456 0.4085 171 P 0.0328 0.5853 0.3820 172 K 0.0465 0.5493 0.4043 173 A 0.0447 0.4821 0.4732 174 R 0.0557 0.3846 0.5597 175 L 0.0394 0.5338 0.4268 176 E 0.0383 0.5930 0.3687 177 H 0.0319 0.6452 0.3228 178 H 0.0379 0.6349 0.3272 179 H 0.0342 0.6086 0.3572 180 H 0.0358 0.4701 0.4940 181 H 0.0470 0.2839 0.6691 182 H 0.0383 0.1027 0.8590