# This file is the result of combining several RDB files, specifically # T0507.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0507.t2k.stride-ebghtl.rdb (weight 1.24869) # T0507.t2k.str2.rdb (weight 1.54758) # T0507.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 T0507.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0507 # 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 T0507.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 641 # # ============================================ # Comments from T0507.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0507 # 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 T0507.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 641 # # ============================================ # Comments from T0507.t2k.str2.rdb # ============================================ # TARGET T0507 # 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 T0507.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 641 # # ============================================ # Comments from T0507.t2k.alpha.rdb # ============================================ # TARGET T0507 # 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 T0507.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 641 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1703 0.0207 0.8089 2 K 0.7635 0.0078 0.2287 3 V 0.8921 0.0042 0.1037 4 A 0.8951 0.0060 0.0989 5 L 0.8150 0.0193 0.1656 6 G 0.4758 0.0315 0.4928 7 G 0.2019 0.0449 0.7532 8 T 0.1890 0.0995 0.7115 9 F 0.1690 0.2050 0.6261 10 E 0.1073 0.2138 0.6789 11 P 0.0387 0.4427 0.5186 12 L 0.0460 0.4548 0.4992 13 H 0.0483 0.5257 0.4261 14 E 0.0082 0.8371 0.1546 15 G 0.0096 0.8659 0.1245 16 H 0.0054 0.9470 0.0476 17 K 0.0047 0.9598 0.0355 18 K 0.0047 0.9601 0.0352 19 L 0.0047 0.9589 0.0364 20 I 0.0047 0.9594 0.0359 21 D 0.0047 0.9574 0.0379 22 V 0.0048 0.9562 0.0391 23 A 0.0049 0.9510 0.0441 24 I 0.0053 0.9312 0.0635 25 K 0.0068 0.8380 0.1553 26 L 0.0174 0.5832 0.3995 27 G 0.0521 0.1401 0.8077 28 G 0.0389 0.0680 0.8931 29 R 0.2858 0.0251 0.6890 30 D 0.6892 0.0106 0.3002 31 I 0.8926 0.0033 0.1040 32 T 0.9259 0.0034 0.0707 33 I 0.9211 0.0033 0.0756 34 G 0.8817 0.0049 0.1134 35 V 0.6472 0.0097 0.3431 36 T 0.2324 0.0312 0.7364 37 S 0.0726 0.0760 0.8513 38 D 0.0304 0.2955 0.6740 39 R 0.0420 0.3780 0.5799 40 M 0.0481 0.4873 0.4646 41 A 0.0438 0.4868 0.4695 42 R 0.0598 0.4302 0.5100 43 A 0.0831 0.2437 0.6733 44 R 0.0744 0.1264 0.7992 45 I 0.0780 0.0746 0.8474 46 R 0.1429 0.0348 0.8222 47 S 0.1659 0.0250 0.8092 48 V 0.2461 0.0230 0.7309 49 L 0.1640 0.0158 0.8202 50 P 0.0798 0.0242 0.8961 51 F 0.0052 0.9319 0.0629 52 A 0.0048 0.9481 0.0471 53 I 0.0050 0.9494 0.0456 54 R 0.0047 0.9562 0.0391 55 A 0.0047 0.9570 0.0382 56 E 0.0048 0.9548 0.0404 57 N 0.0050 0.9524 0.0426 58 V 0.0054 0.9493 0.0453 59 K 0.0056 0.9454 0.0490 60 R 0.0058 0.9197 0.0745 61 Y 0.0120 0.8374 0.1506 62 V 0.0336 0.6561 0.3103 63 M 0.0535 0.4155 0.5310 64 R 0.0861 0.1792 0.7347 65 K 0.0965 0.0609 0.8426 66 Y 0.1078 0.1456 0.7466 67 G 0.4371 0.0759 0.4870 68 F 0.7066 0.0250 0.2684 69 E 0.8056 0.0143 0.1800 70 P 0.8035 0.0171 0.1794 71 E 0.7424 0.0168 0.2408 72 I 0.6752 0.0292 0.2956 73 V 0.5507 0.0348 0.4145 74 K 0.4747 0.0568 0.4685 75 I 0.3077 0.0941 0.5982 76 T 0.1706 0.0740 0.7554 77 N 0.1230 0.0688 0.8082 78 P 0.1071 0.1024 0.7904 79 Y 0.1315 0.0857 0.7829 80 G 0.1452 0.0894 0.7653 81 K 0.2292 0.0980 0.6728 82 T 0.3525 0.0862 0.5613 83 L 0.4166 0.0905 0.4929 84 D 0.4100 0.0715 0.5186 85 V 0.2962 0.0937 0.6101 86 D 0.2494 0.0331 0.7175 87 F 0.3002 0.0179 0.6819 88 E 0.4613 0.0414 0.4973 89 Y 0.9070 0.0045 0.0885 90 L 0.9241 0.0040 0.0719 91 V 0.9192 0.0047 0.0761 92 V 0.8144 0.0136 0.1720 93 S 0.3319 0.0209 0.6472 94 P 0.0763 0.2360 0.6877 95 E 0.1027 0.2794 0.6179 96 T 0.1058 0.2821 0.6121 97 Y 0.0723 0.2795 0.6482 98 E 0.0417 0.3194 0.6388 99 M 0.0375 0.3602 0.6023 100 A 0.0326 0.6653 0.3021 101 L 0.0320 0.8089 0.1591 102 K 0.0183 0.8824 0.0992 103 I 0.0087 0.9243 0.0670 104 N 0.0074 0.9331 0.0594 105 Q 0.0068 0.9441 0.0491 106 K 0.0062 0.9519 0.0419 107 R 0.0057 0.9514 0.0429 108 E 0.0057 0.9361 0.0583 109 E 0.0068 0.8781 0.1151 110 L 0.0412 0.4580 0.5008 111 G 0.0344 0.0595 0.9062 112 K 0.0579 0.0344 0.9077 113 R 0.1084 0.0344 0.8572 114 K 0.1673 0.1137 0.7190 115 I 0.3239 0.0937 0.5824 116 T 0.6876 0.0348 0.2776 117 I 0.8343 0.0055 0.1603 118 V 0.8891 0.0051 0.1058 119 K 0.9112 0.0038 0.0850 120 V 0.8572 0.0067 0.1362 121 D 0.8148 0.0079 0.1773 122 W 0.7838 0.0114 0.2049 123 M 0.7564 0.0131 0.2306 124 M 0.6614 0.0158 0.3228 125 A 0.2112 0.0624 0.7263 126 E 0.0432 0.1423 0.8145 127 D 0.0546 0.0711 0.8743 128 G 0.0666 0.0484 0.8849 129 K 0.2660 0.0260 0.7080 130 P 0.5872 0.0229 0.3900 131 I 0.5662 0.0376 0.3962 132 S 0.5416 0.0449 0.4135 133 S 0.5701 0.0955 0.3344 134 T 0.6600 0.0826 0.2574 135 R 0.7564 0.0514 0.1923 136 I 0.7144 0.0472 0.2384 137 K 0.5375 0.0682 0.3943 138 R 0.2442 0.0816 0.6743 139 G 0.2253 0.0520 0.7228 140 E 0.4261 0.0309 0.5430 141 I 0.6858 0.0158 0.2984 142 D 0.1676 0.0251 0.8073 143 R 0.0286 0.1251 0.8463 144 Y 0.0503 0.0259 0.9239 145 G 0.0581 0.0462 0.8957 146 G 0.1425 0.0507 0.8069 147 I 0.3780 0.0481 0.5739 148 I 0.0571 0.0258 0.9171