# This file is the result of combining several RDB files, specifically # T0299.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0299.t2k.stride-ebghtl.rdb (weight 1.24869) # T0299.t2k.str2.rdb (weight 1.54758) # T0299.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 T0299.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0299 # 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 T0299.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 77 # # ============================================ # Comments from T0299.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0299 # 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 T0299.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 77 # # ============================================ # Comments from T0299.t2k.str2.rdb # ============================================ # TARGET T0299 # 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 T0299.t2k-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 62.9473 # # ============================================ # Comments from T0299.t2k.alpha.rdb # ============================================ # TARGET T0299 # 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 T0299.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 77 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0522 0.0660 0.8818 2 T 0.1572 0.1311 0.7117 3 R 0.3934 0.1787 0.4279 4 Y 0.6297 0.2181 0.1522 5 A 0.7513 0.1668 0.0819 6 L 0.7934 0.1330 0.0736 7 L 0.7963 0.1097 0.0940 8 V 0.7159 0.1067 0.1774 9 R 0.5116 0.1440 0.3444 10 G 0.4621 0.1141 0.4238 11 I 0.5212 0.1318 0.3471 12 N 0.4349 0.0940 0.4712 13 V 0.1638 0.1152 0.7209 14 G 0.0633 0.1083 0.8284 15 G 0.0503 0.1369 0.8128 16 K 0.0795 0.1495 0.7710 17 N 0.1423 0.1380 0.7197 18 K 0.3093 0.0870 0.6037 19 V 0.4408 0.0817 0.4775 20 V 0.2281 0.0982 0.6737 21 M 0.0106 0.8852 0.1042 22 A 0.0053 0.9450 0.0497 23 E 0.0051 0.9502 0.0447 24 L 0.0048 0.9554 0.0398 25 R 0.0047 0.9573 0.0380 26 Q 0.0047 0.9570 0.0383 27 E 0.0048 0.9559 0.0393 28 L 0.0051 0.9515 0.0434 29 T 0.0050 0.9383 0.0567 30 N 0.0059 0.8811 0.1130 31 L 0.0407 0.4894 0.4698 32 G 0.0448 0.0579 0.8973 33 L 0.0828 0.0816 0.8356 34 E 0.1217 0.1807 0.6976 35 K 0.2387 0.1406 0.6207 36 V 0.4942 0.0689 0.4368 37 E 0.6220 0.1077 0.2703 38 S 0.7780 0.0796 0.1424 39 Y 0.7487 0.1035 0.1479 40 I 0.6869 0.1208 0.1923 41 N 0.5627 0.1205 0.3168 42 S 0.3710 0.0836 0.5453 43 G 0.3346 0.0491 0.6164 44 N 0.4493 0.0399 0.5108 45 I 0.7544 0.0321 0.2135 46 F 0.8530 0.0267 0.1203 47 F 0.8095 0.0325 0.1580 48 T 0.5989 0.0344 0.3667 49 S 0.2736 0.0269 0.6995 50 I 0.0702 0.0759 0.8540 51 D 0.0538 0.0704 0.8758 52 S 0.0613 0.0618 0.8769 53 K 0.0057 0.9117 0.0826 54 A 0.0049 0.9388 0.0563 55 Q 0.0049 0.9470 0.0481 56 L 0.0048 0.9533 0.0419 57 V 0.0047 0.9567 0.0386 58 E 0.0049 0.9546 0.0405 59 K 0.0048 0.9564 0.0388 60 L 0.0047 0.9587 0.0366 61 E 0.0047 0.9602 0.0351 62 T 0.0047 0.9583 0.0370 63 F 0.0047 0.9587 0.0366 64 F 0.0047 0.9572 0.0381 65 A 0.0049 0.9461 0.0491 66 V 0.0061 0.9082 0.0857 67 H 0.0104 0.8311 0.1585 68 Y 0.0505 0.4324 0.5170 69 P 0.0407 0.0739 0.8854 70 F 0.0954 0.0515 0.8531 71 I 0.1489 0.0361 0.8150 72 Q 0.2482 0.0207 0.7311 73 S 0.4690 0.0328 0.4983 74 F 0.8688 0.0148 0.1163 75 S 0.9145 0.0072 0.0783 76 L 0.9072 0.0052 0.0876 77 L 0.7522 0.0106 0.2372 78 S 0.2633 0.0124 0.7243 79 L 0.0053 0.8932 0.1015 80 E 0.0048 0.9373 0.0578 81 D 0.0049 0.9462 0.0489 82 F 0.0047 0.9545 0.0407 83 E 0.0047 0.9566 0.0387 84 A 0.0047 0.9547 0.0406 85 E 0.0049 0.9516 0.0435 86 L 0.0053 0.9401 0.0546 87 E 0.0070 0.8550 0.1380 88 N 0.0154 0.6112 0.3735 89 L 0.0783 0.0912 0.8304 90 P 0.0228 0.2133 0.7639 91 A 0.0557 0.2920 0.6523 92 W 0.0648 0.4062 0.5290 93 W 0.0631 0.4292 0.5077 94 S 0.0706 0.3594 0.5700 95 R 0.0892 0.2762 0.6346 96 D 0.0742 0.2330 0.6929 97 L 0.0725 0.2289 0.6986 98 A 0.0834 0.2058 0.7108 99 R 0.1372 0.1534 0.7095 100 K 0.3230 0.0648 0.6122 101 D 0.6283 0.0215 0.3502 102 F 0.8360 0.0106 0.1534 103 L 0.9050 0.0063 0.0887 104 F 0.9106 0.0058 0.0836 105 Y 0.8790 0.0083 0.1127 106 T 0.7227 0.0179 0.2594 107 E 0.3198 0.0476 0.6326 108 G 0.1256 0.0448 0.8296 109 L 0.0843 0.0505 0.8651 110 D 0.0740 0.0735 0.8526 111 V 0.0478 0.2700 0.6822 112 D 0.0377 0.5180 0.4443 113 Q 0.0149 0.7675 0.2176 114 V 0.0154 0.8116 0.1730 115 I 0.0185 0.8510 0.1305 116 A 0.0253 0.8323 0.1423 117 T 0.0214 0.8182 0.1604 118 V 0.0232 0.7882 0.1886 119 E 0.0319 0.7210 0.2471 120 S 0.0314 0.6360 0.3326 121 L 0.0430 0.4660 0.4910 122 E 0.0601 0.3024 0.6375 123 L 0.0650 0.2258 0.7091 124 K 0.0818 0.1804 0.7378 125 D 0.1625 0.1451 0.6924 126 E 0.4612 0.1185 0.4203 127 V 0.7595 0.0642 0.1763 128 L 0.8112 0.0454 0.1434 129 Y 0.8246 0.0275 0.1480 130 F 0.6931 0.0349 0.2720 131 G 0.3330 0.0403 0.6267 132 K 0.1500 0.0518 0.7981 133 L 0.3225 0.0445 0.6330 134 G 0.8608 0.0049 0.1343 135 I 0.9262 0.0033 0.0706 136 F 0.9290 0.0033 0.0677 137 W 0.9205 0.0038 0.0757 138 G 0.8664 0.0055 0.1282 139 K 0.6284 0.0103 0.3614 140 F 0.3361 0.0580 0.6059 141 S 0.1451 0.0843 0.7705 142 E 0.0834 0.1084 0.8082 143 E 0.1114 0.1541 0.7344 144 S 0.1425 0.1447 0.7128 145 Y 0.1504 0.1890 0.6606 146 S 0.1666 0.2459 0.5875 147 K 0.1209 0.3464 0.5327 148 T 0.0828 0.4019 0.5153 149 A 0.0539 0.6186 0.3275 150 Y 0.0602 0.6809 0.2589 151 H 0.0477 0.7106 0.2417 152 K 0.0465 0.7084 0.2452 153 Y 0.0557 0.7178 0.2265 154 L 0.0775 0.7020 0.2205 155 L 0.1147 0.6012 0.2841 156 K 0.1263 0.5170 0.3567 157 V 0.1208 0.4462 0.4330 158 P 0.1394 0.3952 0.4654 159 F 0.1034 0.3212 0.5754 160 Y 0.1078 0.1282 0.7640 161 R 0.1876 0.0904 0.7220 162 H 0.3428 0.1207 0.5365 163 I 0.3904 0.1804 0.4292 164 T 0.4030 0.2499 0.3471 165 I 0.3411 0.3450 0.3139 166 R 0.2023 0.3979 0.3998 167 N 0.1344 0.4502 0.4154 168 A 0.0141 0.7983 0.1877 169 K 0.0114 0.8611 0.1276 170 T 0.0062 0.9217 0.0721 171 F 0.0047 0.9545 0.0408 172 D 0.0047 0.9592 0.0361 173 K 0.0047 0.9588 0.0366 174 I 0.0047 0.9563 0.0390 175 G 0.0048 0.9501 0.0451 176 Q 0.0050 0.9272 0.0679 177 M 0.0069 0.8806 0.1125 178 L 0.0387 0.6543 0.3070 179 K 0.0260 0.2909 0.6831 180 K 0.0293 0.0493 0.9214