# This file is the result of combining several RDB files, specifically # T0285.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0285.t2k.stride-ebghtl.rdb (weight 1.24869) # T0285.t2k.str2.rdb (weight 1.54758) # T0285.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 T0285.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0285 # 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 T0285.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 1 # # ============================================ # Comments from T0285.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0285 # 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 T0285.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 1 # # ============================================ # Comments from T0285.t2k.str2.rdb # ============================================ # TARGET T0285 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0285.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 1 # # ============================================ # Comments from T0285.t2k.alpha.rdb # ============================================ # TARGET T0285 # 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 T0285.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0960 0.0673 0.8367 2 Y 0.2030 0.0504 0.7466 3 L 0.1343 0.0419 0.8238 4 P 0.0676 0.0876 0.8448 5 D 0.0474 0.1210 0.8316 6 D 0.0415 0.1223 0.8362 7 S 0.0524 0.1148 0.8328 8 P 0.0333 0.4907 0.4761 9 A 0.0298 0.7312 0.2390 10 K 0.0249 0.8261 0.1490 11 R 0.0323 0.8642 0.1035 12 L 0.0410 0.8748 0.0842 13 L 0.0451 0.8799 0.0750 14 F 0.0592 0.8599 0.0809 15 Q 0.0629 0.8314 0.1056 16 M 0.0612 0.7847 0.1542 17 V 0.0789 0.6869 0.2342 18 G 0.0618 0.6382 0.3000 19 N 0.0561 0.6344 0.3095 20 A 0.0741 0.6483 0.2776 21 I 0.1035 0.5775 0.3190 22 N 0.0921 0.4450 0.4629 23 R 0.0452 0.5046 0.4502 24 N 0.0537 0.4548 0.4915 25 T 0.0524 0.6065 0.3411 26 Q 0.0591 0.6492 0.2917 27 Q 0.0833 0.6465 0.2701 28 L 0.1017 0.6163 0.2820 29 T 0.1077 0.5643 0.3280 30 Q 0.0775 0.6490 0.2735 31 D 0.0598 0.6376 0.3026 32 L 0.0589 0.6382 0.3029 33 R 0.0782 0.5365 0.3853 34 A 0.0874 0.4269 0.4857 35 M 0.0774 0.1670 0.7557 36 P 0.0494 0.1948 0.7558 37 N 0.0748 0.1564 0.7688 38 W 0.1940 0.1447 0.6613 39 S 0.4382 0.0836 0.4783 40 L 0.7090 0.0510 0.2400 41 R 0.7579 0.0444 0.1977 42 F 0.8702 0.0188 0.1110 43 V 0.8872 0.0163 0.0964 44 Y 0.8952 0.0133 0.0915 45 I 0.8818 0.0156 0.1026 46 V 0.7879 0.0315 0.1806 47 D 0.4969 0.0426 0.4605 48 R 0.1335 0.1373 0.7292 49 N 0.0643 0.1032 0.8326 50 N 0.0751 0.1393 0.7856 51 Q 0.0813 0.2877 0.6310 52 D 0.1428 0.3498 0.5074 53 L 0.1503 0.4054 0.4443 54 L 0.1774 0.2914 0.5312 55 K 0.1517 0.2074 0.6409 56 R 0.1150 0.0849 0.8001 57 P 0.1047 0.0557 0.8397 58 L 0.1368 0.0416 0.8217 59 P 0.0798 0.0413 0.8789 60 P 0.0662 0.1374 0.7964 61 G 0.1420 0.1217 0.7363 62 I 0.5365 0.0819 0.3815 63 M 0.7694 0.0386 0.1919 64 V 0.7762 0.0415 0.1823 65 L 0.6689 0.0572 0.2740 66 A 0.3765 0.0661 0.5574 67 P 0.2102 0.1767 0.6131 68 R 0.2321 0.2159 0.5519 69 L 0.2835 0.1980 0.5185 70 T 0.2191 0.1864 0.5945 71 A 0.1752 0.1732 0.6516 72 K 0.1074 0.1447 0.7478 73 H 0.0966 0.0794 0.8239 74 P 0.0716 0.1946 0.7338 75 Y 0.0715 0.3289 0.5996 76 D 0.0711 0.4232 0.5058 77 K 0.0987 0.4613 0.4400 78 V 0.1263 0.4540 0.4197 79 Q 0.1174 0.4268 0.4558 80 D 0.1121 0.4140 0.4739 81 R 0.0712 0.4289 0.5000 82 N 0.0819 0.3102 0.6079 83 R 0.1302 0.2868 0.5830 84 K 0.2256 0.2784 0.4960 85 L 0.2666 0.2381 0.4953 86 Y 0.2862 0.1388 0.5750 87 G 0.2763 0.0914 0.6323 88 R 0.4040 0.0781 0.5179 89 H 0.6284 0.0344 0.3371 90 I 0.7669 0.0179 0.2153 91 T 0.7822 0.0130 0.2048 92 L 0.5757 0.0538 0.3705 93 N 0.2783 0.0918 0.6299 94 D 0.1171 0.0992 0.7837 95 G 0.0878 0.0657 0.8465 96 N 0.1850 0.0477 0.7673 97 S 0.5562 0.0206 0.4232 98 V 0.7913 0.0059 0.2028 99 K 0.8797 0.0056 0.1147 100 V 0.9163 0.0033 0.0803 101 V 0.9013 0.0055 0.0932 102 T 0.8966 0.0042 0.0992 103 I 0.8093 0.0139 0.1769 104 S 0.6149 0.0295 0.3557 105 A 0.2945 0.0765 0.6290 106 G 0.1411 0.0683 0.7907 107 R 0.1185 0.0911 0.7904 108 D 0.1148 0.0968 0.7884 109 E 0.1091 0.0983 0.7926 110 G 0.0640 0.0695 0.8664 111 P 0.0558 0.1488 0.7954 112 D 0.0645 0.2306 0.7049 113 R 0.0355 0.5668 0.3976 114 D 0.0400 0.7282 0.2318 115 I 0.0436 0.8441 0.1123 116 I 0.0351 0.8900 0.0750 117 W 0.0271 0.9094 0.0635 118 E 0.0264 0.9098 0.0638 119 M 0.0182 0.9055 0.0763 120 F 0.0214 0.8755 0.1030 121 L 0.0232 0.8286 0.1482 122 E 0.0244 0.6877 0.2879 123 N 0.0391 0.3956 0.5653 124 L 0.0602 0.1876 0.7522 125 E 0.0347 0.1286 0.8367