# This file is the result of combining several RDB files, specifically # T0346.t04.dssp-ebghstl.rdb (weight 1.53986) # T0346.t04.stride-ebghtl.rdb (weight 1.24869) # T0346.t04.str2.rdb (weight 1.54758) # T0346.t04.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 T0346.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0346 # 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 T0346.t04-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 88.9705 # # ============================================ # Comments from T0346.t04.stride-ebghtl.rdb # ============================================ # TARGET T0346 # Using neural net t04-2621-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 T0346.t04-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 88.9705 # # ============================================ # Comments from T0346.t04.str2.rdb # ============================================ # TARGET T0346 # Using neural net t04-2621-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 T0346.t04-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 88.9705 # # ============================================ # Comments from T0346.t04.alpha.rdb # ============================================ # TARGET T0346 # Using neural net t04-2621-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 T0346.t04-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 88.9705 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0885 0.0105 0.9010 2 P 0.1318 0.0583 0.8099 3 Q 0.3458 0.0725 0.5817 4 C 0.5851 0.0360 0.3790 5 H 0.6717 0.0277 0.3006 6 F 0.7115 0.0194 0.2691 7 D 0.7011 0.0201 0.2787 8 I 0.7707 0.0238 0.2055 9 E 0.8150 0.0214 0.1635 10 I 0.7899 0.0301 0.1799 11 N 0.5917 0.0247 0.3836 12 R 0.3993 0.0293 0.5714 13 E 0.3208 0.0155 0.6637 14 P 0.2995 0.0379 0.6627 15 V 0.2426 0.0716 0.6858 16 G 0.4288 0.0280 0.5433 17 R 0.7201 0.0115 0.2684 18 I 0.9073 0.0037 0.0891 19 M 0.9267 0.0038 0.0695 20 F 0.9279 0.0037 0.0684 21 Q 0.9034 0.0060 0.0906 22 L 0.7596 0.0176 0.2228 23 F 0.3425 0.0515 0.6060 24 S 0.0671 0.3391 0.5939 25 D 0.0362 0.3619 0.6019 26 I 0.0541 0.3849 0.5610 27 C 0.0539 0.2091 0.7370 28 P 0.0211 0.6310 0.3479 29 K 0.0161 0.8878 0.0961 30 T 0.0151 0.9100 0.0749 31 C 0.0094 0.9433 0.0473 32 K 0.0071 0.9448 0.0481 33 N 0.0064 0.9351 0.0585 34 F 0.0064 0.9400 0.0535 35 L 0.0075 0.9429 0.0496 36 C 0.0079 0.9412 0.0509 37 L 0.0073 0.9222 0.0705 38 C 0.0198 0.7932 0.1871 39 S 0.0607 0.4461 0.4932 40 G 0.0499 0.1455 0.8046 41 E 0.0718 0.1413 0.7869 42 K 0.0762 0.1594 0.7644 43 G 0.0932 0.1186 0.7882 44 L 0.1796 0.0987 0.7217 45 G 0.2197 0.0727 0.7076 46 K 0.1359 0.1530 0.7111 47 T 0.1368 0.1627 0.7005 48 T 0.1009 0.1060 0.7931 49 G 0.1031 0.0607 0.8363 50 K 0.3074 0.0476 0.6450 51 K 0.5252 0.0610 0.4139 52 L 0.5666 0.1096 0.3239 53 C 0.5468 0.0884 0.3648 54 Y 0.4205 0.0983 0.4812 55 K 0.1011 0.0852 0.8137 56 G 0.0627 0.0418 0.8955 57 S 0.3382 0.0252 0.6366 58 T 0.6759 0.0308 0.2933 59 F 0.7356 0.0671 0.1973 60 H 0.7133 0.0883 0.1984 61 R 0.6978 0.0793 0.2229 62 V 0.7003 0.0677 0.2320 63 V 0.5725 0.0669 0.3607 64 K 0.2797 0.1712 0.5491 65 N 0.2344 0.1296 0.6360 66 F 0.5992 0.0708 0.3299 67 M 0.8143 0.0244 0.1613 68 I 0.8284 0.0189 0.1527 69 Q 0.6923 0.0295 0.2782 70 G 0.3713 0.0411 0.5876 71 G 0.2137 0.0408 0.7455 72 D 0.2654 0.0438 0.6908 73 F 0.1849 0.0745 0.7406 74 S 0.1511 0.0853 0.7636 75 E 0.1270 0.0937 0.7793 76 G 0.1160 0.0654 0.8186 77 N 0.1288 0.0455 0.8257 78 G 0.1136 0.0545 0.8318 79 K 0.1639 0.0434 0.7927 80 G 0.1618 0.0463 0.7919 81 G 0.1909 0.0462 0.7629 82 E 0.3409 0.0684 0.5907 83 S 0.3333 0.0833 0.5834 84 I 0.2726 0.1408 0.5867 85 Y 0.1816 0.1005 0.7179 86 G 0.0940 0.0724 0.8336 87 G 0.1351 0.0545 0.8104 88 Y 0.2747 0.0736 0.6517 89 F 0.2104 0.0988 0.6908 90 K 0.1378 0.1887 0.6735 91 D 0.0981 0.2402 0.6617 92 E 0.0900 0.3561 0.5539 93 N 0.1141 0.2878 0.5982 94 F 0.1368 0.2326 0.6306 95 I 0.2109 0.2177 0.5714 96 L 0.2688 0.1699 0.5613 97 K 0.1878 0.1941 0.6181 98 H 0.1277 0.1592 0.7131 99 D 0.0950 0.0976 0.8073 100 R 0.1315 0.1682 0.7003 101 A 0.2592 0.1689 0.5719 102 F 0.5582 0.1085 0.3333 103 L 0.7753 0.0774 0.1473 104 L 0.7927 0.0976 0.1097 105 S 0.7159 0.1438 0.1403 106 M 0.6637 0.1570 0.1793 107 A 0.5797 0.1636 0.2567 108 N 0.3814 0.1438 0.4748 109 R 0.1624 0.1186 0.7189 110 G 0.0721 0.0299 0.8980 111 K 0.0563 0.0704 0.8733 112 H 0.0633 0.0593 0.8774 113 T 0.1009 0.0765 0.8226 114 N 0.1047 0.0913 0.8040 115 G 0.1154 0.0822 0.8024 116 S 0.2617 0.0532 0.6851 117 Q 0.5722 0.0401 0.3877 118 F 0.8301 0.0182 0.1518 119 F 0.8909 0.0163 0.0928 120 I 0.8910 0.0157 0.0933 121 T 0.8131 0.0180 0.1690 122 T 0.5477 0.0234 0.4290 123 K 0.2760 0.0303 0.6937 124 P 0.2113 0.0400 0.7487 125 A 0.1228 0.0708 0.8064 126 P 0.0769 0.2536 0.6695 127 H 0.0757 0.2871 0.6372 128 L 0.1455 0.1476 0.7070 129 D 0.0664 0.0648 0.8687 130 G 0.0616 0.0553 0.8831 131 V 0.2301 0.0399 0.7299 132 H 0.7264 0.0097 0.2638 133 V 0.8280 0.0081 0.1638 134 V 0.8615 0.0112 0.1273 135 F 0.7493 0.0449 0.2058 136 G 0.6605 0.0452 0.2943 137 L 0.7590 0.0474 0.1935 138 V 0.7751 0.0625 0.1625 139 I 0.4557 0.1879 0.3564 140 S 0.1905 0.2725 0.5370 141 G 0.0403 0.4936 0.4661 142 F 0.0158 0.8626 0.1216 143 E 0.0134 0.9079 0.0787 144 V 0.0086 0.9354 0.0560 145 I 0.0085 0.9447 0.0467 146 E 0.0079 0.9431 0.0490 147 Q 0.0079 0.9358 0.0563 148 I 0.0085 0.9050 0.0865 149 E 0.0109 0.8028 0.1863 150 N 0.0155 0.5587 0.4257 151 L 0.0814 0.1412 0.7774 152 K 0.1059 0.0551 0.8389 153 T 0.1814 0.0593 0.7593 154 D 0.1167 0.0757 0.8076 155 A 0.0397 0.2673 0.6930 156 A 0.0466 0.1615 0.7919 157 S 0.0587 0.0908 0.8505 158 R 0.1648 0.0134 0.8218 159 P 0.2990 0.0110 0.6900 160 Y 0.3086 0.0386 0.6528 161 A 0.3861 0.0342 0.5797 162 D 0.5111 0.0191 0.4698 163 V 0.6424 0.0068 0.3508 164 R 0.8627 0.0047 0.1326 165 V 0.8976 0.0034 0.0990 166 I 0.8241 0.0245 0.1513 167 D 0.7470 0.0149 0.2380 168 C 0.6824 0.0368 0.2808 169 G 0.6736 0.0371 0.2892 170 V 0.6502 0.0373 0.3125 171 L 0.3301 0.0391 0.6308 172 A 0.1200 0.0225 0.8575