# This file is the result of combining several RDB files, specifically # T0290.t06.dssp-ebghstl.rdb (weight 1.53986) # T0290.t06.stride-ebghtl.rdb (weight 1.24869) # T0290.t06.str2.rdb (weight 1.54758) # T0290.t06.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 T0290.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0290 # 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 T0290.t06-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 90.6897 # # ============================================ # Comments from T0290.t06.stride-ebghtl.rdb # ============================================ # TARGET T0290 # Using neural net t06-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 T0290.t06-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 90.6897 # # ============================================ # Comments from T0290.t06.str2.rdb # ============================================ # TARGET T0290 # 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 T0290.t06-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 90.6897 # # ============================================ # Comments from T0290.t06.alpha.rdb # ============================================ # TARGET T0290 # Using neural net t06-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 T0290.t06-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 90.6897 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.0687 0.0124 0.9189 2 P 0.1012 0.0575 0.8414 3 R 0.2710 0.0806 0.6484 4 C 0.5167 0.0570 0.4263 5 F 0.5912 0.0578 0.3510 6 F 0.6031 0.0492 0.3477 7 D 0.6455 0.0536 0.3009 8 I 0.7486 0.0647 0.1867 9 A 0.7886 0.0618 0.1496 10 I 0.7541 0.0693 0.1766 11 N 0.4942 0.0543 0.4515 12 N 0.2599 0.0337 0.7063 13 Q 0.2709 0.0178 0.7113 14 P 0.2298 0.0474 0.7229 15 A 0.1805 0.0689 0.7506 16 G 0.3845 0.0296 0.5860 17 R 0.6779 0.0079 0.3142 18 V 0.9118 0.0034 0.0848 19 V 0.9283 0.0035 0.0683 20 F 0.9291 0.0033 0.0676 21 E 0.9127 0.0042 0.0831 22 L 0.7692 0.0170 0.2138 23 F 0.3015 0.0336 0.6649 24 S 0.0699 0.2826 0.6475 25 D 0.0326 0.3461 0.6214 26 V 0.0459 0.3749 0.5792 27 C 0.0503 0.2187 0.7310 28 P 0.0229 0.6397 0.3374 29 K 0.0268 0.8272 0.1460 30 T 0.0283 0.8710 0.1007 31 C 0.0125 0.9293 0.0581 32 E 0.0072 0.9345 0.0583 33 N 0.0065 0.9241 0.0694 34 F 0.0053 0.9443 0.0504 35 R 0.0053 0.9503 0.0443 36 C 0.0058 0.9506 0.0436 37 L 0.0064 0.9387 0.0550 38 C 0.0157 0.8669 0.1174 39 T 0.0483 0.5695 0.3822 40 G 0.0441 0.1549 0.8010 41 E 0.0586 0.1182 0.8232 42 K 0.1042 0.1033 0.7925 43 G 0.1342 0.0981 0.7677 44 T 0.1648 0.0974 0.7378 45 G 0.1655 0.0898 0.7447 46 K 0.1290 0.1747 0.6963 47 S 0.1524 0.1646 0.6829 48 T 0.1377 0.1248 0.7374 49 Q 0.1192 0.0718 0.8090 50 K 0.2007 0.0325 0.7668 51 P 0.3029 0.0521 0.6450 52 L 0.4370 0.0998 0.4632 53 H 0.4390 0.0960 0.4650 54 Y 0.3585 0.1205 0.5209 55 K 0.1086 0.1156 0.7758 56 S 0.0884 0.0548 0.8569 57 C 0.4340 0.0316 0.5344 58 L 0.7102 0.0415 0.2483 59 F 0.7448 0.0611 0.1941 60 H 0.7273 0.0670 0.2057 61 R 0.7448 0.0561 0.1991 62 V 0.7536 0.0421 0.2043 63 V 0.5818 0.0503 0.3679 64 K 0.2311 0.1540 0.6149 65 D 0.1941 0.1175 0.6885 66 F 0.5468 0.0714 0.3818 67 M 0.8163 0.0199 0.1638 68 V 0.8366 0.0151 0.1483 69 Q 0.6820 0.0320 0.2861 70 G 0.3573 0.0401 0.6026 71 G 0.1990 0.0401 0.7609 72 D 0.2459 0.0355 0.7185 73 F 0.1358 0.1376 0.7265 74 S 0.1263 0.1350 0.7387 75 E 0.1205 0.1067 0.7728 76 G 0.0977 0.0569 0.8453 77 N 0.1146 0.0451 0.8403 78 G 0.1173 0.0527 0.8300 79 R 0.1885 0.0621 0.7495 80 G 0.1709 0.0536 0.7755 81 G 0.1966 0.0476 0.7558 82 E 0.3233 0.0629 0.6139 83 S 0.3128 0.0753 0.6118 84 I 0.2826 0.1275 0.5899 85 Y 0.1798 0.0981 0.7222 86 G 0.0875 0.0632 0.8493 87 G 0.1538 0.0484 0.7978 88 F 0.3281 0.0515 0.6204 89 F 0.2233 0.0915 0.6852 90 E 0.1451 0.1980 0.6569 91 D 0.1197 0.2199 0.6605 92 E 0.1297 0.2770 0.5933 93 S 0.1474 0.2290 0.6236 94 F 0.1690 0.1978 0.6332 95 A 0.2154 0.1848 0.5998 96 V 0.3106 0.1571 0.5323 97 K 0.2715 0.1597 0.5687 98 H 0.2362 0.1524 0.6115 99 N 0.1546 0.0980 0.7475 100 A 0.1516 0.1475 0.7009 101 A 0.2571 0.1586 0.5843 102 F 0.5186 0.1371 0.3443 103 L 0.7270 0.1289 0.1440 104 L 0.7448 0.1438 0.1114 105 S 0.6916 0.1678 0.1406 106 M 0.6214 0.1897 0.1889 107 A 0.5141 0.2119 0.2740 108 N 0.3357 0.1885 0.4758 109 R 0.1909 0.1201 0.6889 110 G 0.0859 0.0323 0.8817 111 K 0.0576 0.0679 0.8745 112 D 0.0686 0.0553 0.8761 113 T 0.1103 0.0698 0.8199 114 N 0.1054 0.0586 0.8361 115 G 0.1190 0.0609 0.8201 116 S 0.2767 0.0411 0.6822 117 Q 0.5979 0.0320 0.3700 118 F 0.8318 0.0187 0.1495 119 F 0.8959 0.0140 0.0901 120 I 0.8998 0.0130 0.0872 121 T 0.8555 0.0113 0.1332 122 T 0.6079 0.0233 0.3688 123 K 0.2876 0.0215 0.6909 124 P 0.1872 0.0325 0.7803 125 T 0.1107 0.0454 0.8439 126 P 0.0497 0.2478 0.7025 127 H 0.0569 0.2595 0.6836 128 L 0.1357 0.1631 0.7012 129 D 0.0689 0.0788 0.8523 130 G 0.0548 0.0751 0.8702 131 H 0.1814 0.0643 0.7543 132 H 0.5993 0.0189 0.3819 133 V 0.7493 0.0105 0.2402 134 V 0.8404 0.0116 0.1480 135 F 0.7175 0.0326 0.2499 136 G 0.6477 0.0299 0.3224 137 Q 0.7734 0.0272 0.1994 138 V 0.7979 0.0357 0.1664 139 I 0.5574 0.1039 0.3387 140 S 0.2509 0.1511 0.5980 141 G 0.0508 0.3933 0.5559 142 Q 0.0190 0.8338 0.1472 143 E 0.0197 0.8929 0.0874 144 V 0.0112 0.9321 0.0567 145 V 0.0101 0.9404 0.0495 146 R 0.0096 0.9404 0.0500 147 E 0.0115 0.9259 0.0626 148 I 0.0169 0.8693 0.1138 149 E 0.0194 0.7253 0.2552 150 N 0.0298 0.4878 0.4824 151 Q 0.0790 0.1601 0.7609 152 K 0.1179 0.0653 0.8168 153 T 0.2567 0.0578 0.6855 154 D 0.1221 0.0585 0.8193 155 A 0.0343 0.2490 0.7167 156 A 0.0446 0.1249 0.8305 157 S 0.0579 0.0641 0.8780 158 K 0.1576 0.0134 0.8291 159 P 0.3322 0.0136 0.6541 160 F 0.3703 0.0403 0.5894 161 A 0.5093 0.0410 0.4497 162 E 0.6102 0.0173 0.3725 163 V 0.7349 0.0065 0.2586 164 R 0.8537 0.0057 0.1405 165 I 0.8841 0.0053 0.1106 166 L 0.8109 0.0290 0.1601 167 S 0.7494 0.0142 0.2364 168 C 0.6410 0.0362 0.3228 169 G 0.6256 0.0401 0.3343 170 E 0.6755 0.0304 0.2941 171 L 0.4780 0.0287 0.4933 172 I 0.1340 0.0183 0.8477 173 P 0.0472 0.0264 0.9264