# This file is the result of combining several RDB files, specifically # T0271.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0271.t2k.stride-ebghtl.rdb (weight 1.24869) # T0271.t2k.str2.rdb (weight 1.54758) # T0271.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 T0271.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0271 # 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 T0271.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 22 # # ============================================ # Comments from T0271.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0271 # 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 T0271.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 22 # # ============================================ # Comments from T0271.t2k.str2.rdb # ============================================ # TARGET T0271 # 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 T0271.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 22 # # ============================================ # Comments from T0271.t2k.alpha.rdb # ============================================ # TARGET T0271 # 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 T0271.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 22 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2531 0.0109 0.7360 2 E 0.6347 0.0058 0.3595 3 L 0.7777 0.0070 0.2153 4 K 0.8360 0.0101 0.1539 5 L 0.8874 0.0061 0.1065 6 I 0.8434 0.0050 0.1516 7 P 0.8119 0.0039 0.1842 8 I 0.6205 0.0095 0.3699 9 E 0.3429 0.0376 0.6195 10 K 0.1775 0.0202 0.8023 11 P 0.0760 0.1310 0.7930 12 E 0.0332 0.2172 0.7496 13 N 0.0499 0.1937 0.7564 14 L 0.1802 0.0831 0.7368 15 N 0.4080 0.0642 0.5277 16 V 0.8224 0.0354 0.1422 17 I 0.8729 0.0362 0.0909 18 L 0.7589 0.0822 0.1589 19 G 0.6005 0.0849 0.3147 20 Q 0.2678 0.2608 0.4714 21 A 0.1017 0.4666 0.4317 22 H 0.0656 0.6151 0.3193 23 F 0.0567 0.6617 0.2817 24 I 0.0363 0.7431 0.2206 25 K 0.0351 0.7033 0.2616 26 T 0.0447 0.6763 0.2790 27 V 0.0074 0.9166 0.0760 28 E 0.0075 0.9160 0.0766 29 D 0.0103 0.9167 0.0731 30 L 0.0054 0.9457 0.0489 31 H 0.0049 0.9482 0.0470 32 E 0.0055 0.9451 0.0494 33 A 0.0061 0.9402 0.0537 34 L 0.0108 0.9224 0.0669 35 V 0.0143 0.8701 0.1156 36 T 0.0288 0.7002 0.2710 37 A 0.0657 0.5097 0.4246 38 V 0.0575 0.1174 0.8252 39 P 0.0277 0.1348 0.8375 40 G 0.0387 0.0958 0.8655 41 I 0.3151 0.0292 0.6557 42 R 0.7155 0.0342 0.2504 43 F 0.8938 0.0109 0.0953 44 G 0.8939 0.0160 0.0900 45 L 0.9020 0.0163 0.0817 46 A 0.8793 0.0182 0.1025 47 F 0.8258 0.0253 0.1489 48 S 0.6315 0.0364 0.3320 49 E 0.2893 0.1068 0.6039 50 A 0.1916 0.0839 0.7246 51 S 0.1052 0.0492 0.8455 52 G 0.1056 0.0307 0.8637 53 K 0.2055 0.1097 0.6849 54 R 0.5336 0.0596 0.4067 55 L 0.7526 0.0390 0.2084 56 V 0.7968 0.0278 0.1754 57 R 0.7076 0.0325 0.2599 58 R 0.4573 0.0643 0.4785 59 S 0.1593 0.0793 0.7614 60 G 0.0798 0.0620 0.8582 61 T 0.0890 0.0433 0.8678 62 D 0.0580 0.0888 0.8531 63 E 0.0055 0.9353 0.0592 64 A 0.0055 0.9470 0.0475 65 L 0.0048 0.9522 0.0430 66 V 0.0047 0.9585 0.0367 67 E 0.0048 0.9533 0.0419 68 L 0.0047 0.9564 0.0389 69 A 0.0047 0.9548 0.0405 70 V 0.0047 0.9520 0.0433 71 K 0.0049 0.9414 0.0537 72 N 0.0050 0.9235 0.0715 73 L 0.0062 0.9256 0.0682 74 L 0.0073 0.9071 0.0856 75 N 0.0084 0.8222 0.1694 76 L 0.0262 0.7398 0.2340 77 A 0.0403 0.5073 0.4524 78 C 0.0317 0.4158 0.5524 79 G 0.0624 0.1828 0.7548 80 H 0.3188 0.1862 0.4950 81 V 0.6482 0.1439 0.2079 82 F 0.7769 0.1146 0.1085 83 L 0.8436 0.0707 0.0856 84 I 0.8444 0.0618 0.0938 85 V 0.8009 0.0623 0.1368 86 L 0.5976 0.0979 0.3045 87 G 0.2231 0.1819 0.5950 88 E 0.0960 0.2446 0.6595 89 G 0.0867 0.2882 0.6251 90 F 0.1180 0.2248 0.6572 91 Y 0.1474 0.2137 0.6390 92 P 0.0952 0.5939 0.3109 93 I 0.0566 0.8134 0.1300 94 N 0.0552 0.8230 0.1218 95 V 0.0313 0.8416 0.1270 96 L 0.0226 0.8569 0.1206 97 H 0.0233 0.8445 0.1322 98 A 0.0194 0.8511 0.1295 99 V 0.0316 0.8220 0.1464 100 K 0.0434 0.6416 0.3150 101 A 0.0407 0.4685 0.4908 102 C 0.0661 0.2226 0.7112 103 P 0.0231 0.4225 0.5544 104 E 0.0582 0.4665 0.4754 105 V 0.2639 0.4504 0.2857 106 V 0.4461 0.3127 0.2412 107 R 0.6313 0.2358 0.1329 108 I 0.6501 0.2649 0.0850 109 Y 0.5474 0.3468 0.1058 110 A 0.5685 0.2872 0.1443 111 A 0.4016 0.2549 0.3435 112 T 0.2223 0.2140 0.5637 113 A 0.1183 0.1050 0.7767 114 N 0.1268 0.0225 0.8507 115 P 0.1164 0.1156 0.7680 116 L 0.4502 0.0622 0.4876 117 K 0.7370 0.0529 0.2101 118 V 0.9027 0.0085 0.0887 119 V 0.9227 0.0064 0.0709 120 V 0.9194 0.0067 0.0739 121 A 0.8843 0.0081 0.1075 122 E 0.8136 0.0157 0.1708 123 E 0.4458 0.0183 0.5359 124 G 0.0741 0.1105 0.8155 125 E 0.0998 0.0435 0.8567 126 Q 0.2386 0.0415 0.7199 127 R 0.5590 0.0243 0.4168 128 A 0.8359 0.0095 0.1546 129 I 0.8983 0.0091 0.0926 130 L 0.8580 0.0263 0.1157 131 G 0.8518 0.0138 0.1344 132 V 0.7925 0.0192 0.1883 133 M 0.5947 0.0286 0.3767 134 D 0.2545 0.0542 0.6913 135 G 0.1229 0.0773 0.7999 136 F 0.1446 0.0761 0.7794 137 T 0.1045 0.0675 0.8279 138 P 0.0655 0.1245 0.8101 139 L 0.0803 0.1047 0.8150 140 G 0.1054 0.0803 0.8143 141 V 0.2171 0.0498 0.7330 142 E 0.1830 0.0324 0.7846 143 D 0.0877 0.0394 0.8730 144 E 0.0055 0.9140 0.0805 145 A 0.0049 0.9345 0.0606 146 E 0.0051 0.9461 0.0488 147 V 0.0047 0.9557 0.0396 148 A 0.0050 0.9493 0.0457 149 W 0.0049 0.9405 0.0545 150 R 0.0049 0.9429 0.0522 151 K 0.0051 0.9535 0.0414 152 D 0.0048 0.9500 0.0452 153 L 0.0047 0.9485 0.0468 154 L 0.0048 0.9478 0.0474 155 R 0.0053 0.9324 0.0624 156 R 0.0061 0.9145 0.0794 157 L 0.0405 0.7090 0.2505 158 G 0.0408 0.3272 0.6321 159 Y 0.0973 0.2711 0.6316 160 K 0.1724 0.1871 0.6405 161 L 0.0634 0.0474 0.8892