# This file is the result of combining several RDB files, specifically # T0361.t04.dssp-ebghstl.rdb (weight 1.53986) # T0361.t04.stride-ebghtl.rdb (weight 1.24869) # T0361.t04.str2.rdb (weight 1.54758) # T0361.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 T0361.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0361 # 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 T0361.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 9.29976 # # ============================================ # Comments from T0361.t04.stride-ebghtl.rdb # ============================================ # TARGET T0361 # 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 T0361.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 9.29976 # # ============================================ # Comments from T0361.t04.str2.rdb # ============================================ # TARGET T0361 # 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 T0361.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 9.29976 # # ============================================ # Comments from T0361.t04.alpha.rdb # ============================================ # TARGET T0361 # 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 T0361.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 9.29976 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0714 0.0564 0.8722 2 A 0.1236 0.0901 0.7863 3 T 0.1485 0.1469 0.7046 4 L 0.1508 0.1807 0.6685 5 T 0.1510 0.2215 0.6275 6 E 0.0877 0.3968 0.5155 7 D 0.0690 0.3841 0.5469 8 D 0.0606 0.6057 0.3337 9 V 0.1028 0.7250 0.1723 10 L 0.1072 0.7642 0.1286 11 E 0.0867 0.7459 0.1674 12 Q 0.0877 0.6863 0.2260 13 L 0.0749 0.5405 0.3846 14 D 0.0447 0.4111 0.5442 15 A 0.0252 0.4575 0.5172 16 Q 0.0380 0.4269 0.5350 17 D 0.0227 0.5405 0.4368 18 N 0.0309 0.5873 0.3818 19 L 0.0058 0.9291 0.0651 20 F 0.0048 0.9536 0.0416 21 S 0.0047 0.9593 0.0360 22 F 0.0047 0.9603 0.0351 23 M 0.0047 0.9605 0.0348 24 K 0.0046 0.9607 0.0347 25 T 0.0046 0.9591 0.0362 26 A 0.0046 0.9587 0.0367 27 H 0.0047 0.9606 0.0348 28 S 0.0046 0.9613 0.0341 29 I 0.0046 0.9609 0.0345 30 L 0.0047 0.9588 0.0365 31 L 0.0047 0.9569 0.0385 32 Q 0.0047 0.9472 0.0481 33 G 0.0048 0.9304 0.0648 34 I 0.0048 0.9429 0.0522 35 R 0.0052 0.9250 0.0697 36 Q 0.0060 0.8300 0.1640 37 F 0.0104 0.6899 0.2997 38 L 0.0220 0.6553 0.3227 39 P 0.0209 0.6768 0.3023 40 S 0.0447 0.7117 0.2436 41 L 0.1575 0.5786 0.2639 42 F 0.3490 0.2957 0.3553 43 V 0.3229 0.1473 0.5297 44 D 0.1574 0.0970 0.7455 45 N 0.0645 0.1409 0.7946 46 D 0.0741 0.1974 0.7285 47 E 0.0156 0.7062 0.2782 48 E 0.0207 0.8664 0.1129 49 I 0.0441 0.8784 0.0775 50 V 0.0363 0.9048 0.0589 51 E 0.0427 0.9034 0.0539 52 Y 0.0572 0.8549 0.0880 53 A 0.0855 0.7660 0.1485 54 V 0.0591 0.7844 0.1565 55 K 0.0420 0.8146 0.1435 56 P 0.0216 0.8519 0.1266 57 L 0.0326 0.8163 0.1511 58 L 0.0453 0.7079 0.2468 59 A 0.0368 0.5085 0.4547 60 Q 0.0274 0.2047 0.7679 61 S 0.0619 0.0608 0.8772 62 G 0.0636 0.0203 0.9161 63 P 0.0998 0.0371 0.8631 64 L 0.0574 0.3671 0.5754 65 D 0.0453 0.4774 0.4773 66 D 0.1088 0.5606 0.3306 67 I 0.2091 0.5254 0.2655 68 D 0.2066 0.5925 0.2008 69 V 0.2234 0.6899 0.0867 70 A 0.1852 0.7444 0.0704 71 L 0.2154 0.7225 0.0621 72 R 0.1903 0.7421 0.0676 73 L 0.1560 0.7658 0.0782 74 I 0.1106 0.8056 0.0838 75 Y 0.0787 0.7877 0.1336 76 A 0.0431 0.7573 0.1996 77 L 0.0413 0.5529 0.4058 78 G 0.0696 0.2609 0.6695 79 K 0.1583 0.2953 0.5464 80 M 0.1982 0.1958 0.6060 81 D 0.1132 0.1922 0.6946 82 K 0.0090 0.8910 0.1000 83 W 0.0114 0.8941 0.0945 84 L 0.0133 0.9015 0.0853 85 Y 0.0129 0.9120 0.0751 86 A 0.0117 0.8925 0.0959 87 D 0.0109 0.8820 0.1071 88 I 0.0048 0.9490 0.0462 89 T 0.0047 0.9558 0.0394 90 H 0.0047 0.9553 0.0400 91 F 0.0047 0.9568 0.0385 92 S 0.0047 0.9569 0.0384 93 Q 0.0048 0.9520 0.0432 94 Y 0.0049 0.9493 0.0458 95 W 0.0049 0.9513 0.0438 96 H 0.0049 0.9433 0.0518 97 Y 0.0056 0.9255 0.0688 98 L 0.0187 0.8546 0.1267 99 N 0.0267 0.6480 0.3253 100 E 0.0235 0.4676 0.5088 101 Q 0.0418 0.2339 0.7243 102 D 0.0413 0.1353 0.8234 103 E 0.0603 0.1212 0.8185 104 T 0.1010 0.0549 0.8441 105 P 0.0913 0.1155 0.7932 106 G 0.1144 0.1150 0.7706 107 F 0.1680 0.1105 0.7215 108 A 0.1339 0.1037 0.7624 109 D 0.0911 0.1867 0.7222 110 D 0.0391 0.6222 0.3387 111 I 0.0956 0.7006 0.2038 112 T 0.1157 0.7532 0.1310 113 W 0.0883 0.7817 0.1300 114 D 0.0736 0.7597 0.1667 115 F 0.0405 0.8109 0.1486 116 I 0.0318 0.8233 0.1449 117 S 0.0267 0.7744 0.1989 118 N 0.0396 0.7006 0.2598 119 V 0.1068 0.6372 0.2560 120 N 0.1166 0.6021 0.2813 121 S 0.2035 0.5937 0.2028 122 I 0.2321 0.5973 0.1706 123 T 0.1922 0.5543 0.2536 124 R 0.1112 0.4705 0.4183 125 N 0.0820 0.2821 0.6359 126 A 0.0526 0.4273 0.5202 127 T 0.0658 0.5055 0.4287 128 L 0.0577 0.6561 0.2863 129 Y 0.0385 0.7707 0.1909 130 D 0.0315 0.7958 0.1727 131 A 0.0212 0.8559 0.1229 132 L 0.0253 0.8219 0.1528 133 K 0.0249 0.7474 0.2277 134 A 0.0242 0.6590 0.3168 135 M 0.0441 0.4978 0.4581 136 K 0.0407 0.4259 0.5334 137 F 0.0582 0.3268 0.6150 138 A 0.0257 0.4854 0.4889 139 D 0.0463 0.5107 0.4430 140 F 0.0565 0.7612 0.1823 141 A 0.0482 0.8382 0.1136 142 V 0.0635 0.8532 0.0833 143 W 0.0584 0.8532 0.0884 144 S 0.0365 0.8730 0.0905 145 E 0.0309 0.8814 0.0877 146 A 0.0399 0.8503 0.1098 147 R 0.0379 0.8227 0.1394 148 F 0.0256 0.8191 0.1553 149 S 0.0308 0.6972 0.2720 150 G 0.0323 0.5827 0.3850 151 M 0.0997 0.6922 0.2081 152 V 0.1287 0.7476 0.1236 153 K 0.0467 0.8816 0.0717 154 T 0.0192 0.9267 0.0542 155 A 0.0087 0.9506 0.0407 156 L 0.0069 0.9557 0.0374 157 T 0.0055 0.9587 0.0358 158 L 0.0054 0.9588 0.0357 159 A 0.0047 0.9567 0.0387 160 V 0.0047 0.9582 0.0372 161 T 0.0049 0.9592 0.0359 162 T 0.0049 0.9582 0.0369 163 T 0.0048 0.9550 0.0403 164 L 0.0049 0.9480 0.0470 165 K 0.0057 0.9229 0.0714 166 E 0.0089 0.8255 0.1656 167 L 0.0437 0.5072 0.4492 168 T 0.0504 0.0873 0.8624 169 P 0.0201 0.0808 0.8991