# This file is the result of combining several RDB files, specifically # T0316.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0316.t2k.stride-ebghtl.rdb (weight 1.24869) # T0316.t2k.str2.rdb (weight 1.54758) # T0316.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 T0316.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 351 # # ============================================ # Comments from T0316.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 351 # # ============================================ # Comments from T0316.t2k.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 351 # # ============================================ # Comments from T0316.t2k.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 351 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1911 0.0909 0.7180 2 Y 0.6409 0.0498 0.3093 3 V 0.7733 0.0379 0.1888 4 A 0.7336 0.0403 0.2261 5 T 0.5463 0.0462 0.4075 6 G 0.3492 0.0487 0.6021 7 H 0.4308 0.0720 0.4973 8 Y 0.7208 0.0355 0.2438 9 A 0.8395 0.0170 0.1436 10 R 0.8784 0.0122 0.1094 11 V 0.8868 0.0080 0.1052 12 A 0.8660 0.0134 0.1206 13 R 0.8340 0.0131 0.1529 14 D 0.3740 0.0260 0.6000 15 E 0.0461 0.0758 0.8781 16 D 0.0502 0.0233 0.9265 17 G 0.0755 0.0337 0.8907 18 T 0.4771 0.0124 0.5105 19 V 0.8832 0.0048 0.1120 20 H 0.8958 0.0061 0.0980 21 M 0.9131 0.0042 0.0828 22 L 0.8528 0.0130 0.1342 23 R 0.8063 0.0121 0.1815 24 G 0.5929 0.0293 0.3778 25 V 0.3926 0.0393 0.5681 26 D 0.2458 0.0363 0.7180 27 N 0.0429 0.1954 0.7616 28 G 0.0551 0.1395 0.8054 29 K 0.1155 0.1514 0.7331 30 D 0.2409 0.1077 0.6514 31 Q 0.4209 0.2118 0.3674 32 T 0.5680 0.2343 0.1977 33 Y 0.5497 0.3077 0.1426 34 F 0.5314 0.3279 0.1407 35 L 0.4903 0.3032 0.2065 36 S 0.3972 0.2701 0.3327 37 Q 0.3228 0.1849 0.4923 38 L 0.2400 0.0316 0.7284 39 S 0.1179 0.0253 0.8568 40 Q 0.0059 0.8920 0.1021 41 E 0.0051 0.9055 0.0894 42 Q 0.0054 0.9236 0.0710 43 L 0.0066 0.9219 0.0715 44 Q 0.0074 0.8719 0.1207 45 K 0.0109 0.7484 0.2406 46 T 0.0394 0.5685 0.3921 47 M 0.0887 0.3178 0.5935 48 F 0.1171 0.1022 0.7807 49 P 0.1072 0.1293 0.7636 50 L 0.0532 0.3961 0.5507 51 G 0.0470 0.3941 0.5589 52 H 0.0462 0.4601 0.4937 53 L 0.0697 0.2528 0.6775 54 E 0.0714 0.1781 0.7505 55 K 0.0346 0.5918 0.3736 56 P 0.0064 0.9255 0.0681 57 E 0.0052 0.9492 0.0456 58 V 0.0048 0.9558 0.0394 59 R 0.0048 0.9571 0.0381 60 R 0.0048 0.9602 0.0350 61 L 0.0047 0.9605 0.0349 62 A 0.0048 0.9589 0.0364 63 E 0.0050 0.9503 0.0447 64 E 0.0055 0.9159 0.0786 65 A 0.0423 0.3966 0.5612 66 G 0.0341 0.0266 0.9394 67 L 0.0670 0.0255 0.9075 68 S 0.2430 0.0671 0.6900 69 T 0.2964 0.1733 0.5302 70 A 0.2836 0.1465 0.5700 71 K 0.2296 0.0657 0.7047 72 K 0.1763 0.0586 0.7651 73 K 0.1120 0.2008 0.6872 74 D 0.1236 0.1686 0.7078 75 S 0.2010 0.1291 0.6699 76 T 0.1853 0.0800 0.7348 77 G 0.2081 0.0671 0.7248 78 I 0.4932 0.0522 0.4546 79 C 0.5613 0.0588 0.3799 80 F 0.6036 0.0461 0.3502 81 I 0.3940 0.0408 0.5652 82 G 0.1438 0.0407 0.8155 83 E 0.0511 0.1295 0.8194 84 K 0.0638 0.1490 0.7871 85 N 0.0997 0.1894 0.7108 86 F 0.0140 0.8500 0.1360 87 K 0.0057 0.9316 0.0627 88 N 0.0056 0.9438 0.0506 89 F 0.0062 0.9415 0.0522 90 L 0.0068 0.9188 0.0744 91 S 0.0107 0.8348 0.1545 92 N 0.0143 0.7618 0.2239 93 Y 0.0462 0.4973 0.4565 94 L 0.0666 0.1003 0.8331 95 P 0.0747 0.0501 0.8751 96 A 0.1089 0.0660 0.8251 97 Q 0.1264 0.0390 0.8346 98 P 0.2393 0.0450 0.7157 99 G 0.3605 0.0305 0.6090 100 R 0.6514 0.0119 0.3367 101 M 0.7763 0.0062 0.2175 102 M 0.8442 0.0047 0.1511 103 T 0.3676 0.0090 0.6235 104 V 0.0633 0.1085 0.8282 105 D 0.0497 0.0170 0.9332 106 G 0.0534 0.0266 0.9200 107 R 0.3599 0.0084 0.6317 108 D 0.8886 0.0031 0.1083 109 M 0.8445 0.0168 0.1387 110 G 0.8183 0.0140 0.1677 111 E 0.7259 0.0350 0.2391 112 H 0.6508 0.0342 0.3150 113 A 0.4493 0.0663 0.4844 114 G 0.3605 0.0676 0.5719 115 L 0.5987 0.0594 0.3418 116 M 0.6476 0.0716 0.2808 117 Y 0.6974 0.0764 0.2262 118 Y 0.6515 0.0713 0.2772 119 T 0.5664 0.0653 0.3683 120 I 0.4247 0.1890 0.3864 121 G 0.2951 0.2199 0.4850 122 Q 0.3288 0.2669 0.4043 123 R 0.3417 0.2679 0.3903 124 G 0.1282 0.2562 0.6156 125 G 0.0992 0.1674 0.7335 126 L 0.2029 0.1109 0.6862 127 G 0.2714 0.0535 0.6751 128 I 0.3213 0.0691 0.6097 129 G 0.2108 0.0847 0.7045 130 G 0.1494 0.0853 0.7653 131 Q 0.1307 0.0748 0.7944 132 H 0.1275 0.0650 0.8076 133 G 0.1696 0.0655 0.7649 134 G 0.2195 0.0852 0.6954 135 D 0.4880 0.0557 0.4563 136 N 0.7160 0.0271 0.2569 137 A 0.7410 0.0219 0.2371 138 P 0.7359 0.0351 0.2289 139 W 0.5692 0.0823 0.3484 140 F 0.4649 0.0718 0.4633 141 V 0.2736 0.2164 0.5100 142 V 0.1448 0.2923 0.5629 143 G 0.1534 0.2898 0.5568 144 K 0.1086 0.2164 0.6749 145 D 0.1381 0.1681 0.6938 146 L 0.1543 0.1223 0.7234 147 S 0.0735 0.0716 0.8549 148 K 0.0372 0.0532 0.9097