# This file is the result of combining several RDB files, specifically # T0374.t06.dssp-ebghstl.rdb (weight 1.53986) # T0374.t06.stride-ebghtl.rdb (weight 1.24869) # T0374.t06.str2.rdb (weight 1.54758) # T0374.t06.alpha.rdb (weight 0.659012) # T0374.t04.dssp-ebghstl.rdb (weight 1.53986) # T0374.t04.stride-ebghtl.rdb (weight 1.24869) # T0374.t04.str2.rdb (weight 1.54758) # T0374.t04.alpha.rdb (weight 0.659012) # T0374.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0374.t2k.stride-ebghtl.rdb (weight 1.24869) # T0374.t2k.str2.rdb (weight 1.54758) # T0374.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 T0374.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0374 # 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 T0374.t06-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 8826 # # ============================================ # Comments from T0374.t06.stride-ebghtl.rdb # ============================================ # TARGET T0374 # Using neural net t06-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 T0374.t06-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 8826 # # ============================================ # Comments from T0374.t06.str2.rdb # ============================================ # TARGET T0374 # Using neural net t06-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 T0374.t06-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 8826 # # ============================================ # Comments from T0374.t06.alpha.rdb # ============================================ # TARGET T0374 # Using neural net t06-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 T0374.t06-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 8826 # # ============================================ # Comments from T0374.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0374 # 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 T0374.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 2157 # # ============================================ # Comments from T0374.t04.stride-ebghtl.rdb # ============================================ # TARGET T0374 # 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 T0374.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 2157 # # ============================================ # Comments from T0374.t04.str2.rdb # ============================================ # TARGET T0374 # 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 T0374.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 2157 # # ============================================ # Comments from T0374.t04.alpha.rdb # ============================================ # TARGET T0374 # 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 T0374.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 2157 # # ============================================ # Comments from T0374.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0374 # 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 T0374.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 772 # # ============================================ # Comments from T0374.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0374 # 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 T0374.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 772 # # ============================================ # Comments from T0374.t2k.str2.rdb # ============================================ # TARGET T0374 # 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 T0374.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 772 # # ============================================ # Comments from T0374.t2k.alpha.rdb # ============================================ # TARGET T0374 # 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 T0374.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 772 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1181 0.0142 0.8677 2 Q 0.2853 0.0120 0.7027 3 L 0.6924 0.0088 0.2988 4 S 0.8153 0.0099 0.1748 5 H 0.7955 0.0081 0.1965 6 R 0.5534 0.0118 0.4348 7 P 0.3708 0.0135 0.6157 8 A 0.1292 0.0179 0.8529 9 E 0.0741 0.0206 0.9053 10 T 0.0094 0.6705 0.3201 11 G 0.0087 0.6619 0.3295 12 D 0.0233 0.6879 0.2889 13 L 0.0063 0.9057 0.0880 14 E 0.0050 0.9243 0.0707 15 T 0.0051 0.9364 0.0585 16 V 0.0051 0.9490 0.0459 17 A 0.0052 0.9504 0.0443 18 G 0.0055 0.9373 0.0572 19 F 0.0054 0.9283 0.0663 20 P 0.0069 0.9226 0.0705 21 Q 0.0068 0.8929 0.1003 22 D 0.0096 0.8528 0.1376 23 R 0.0134 0.7864 0.2002 24 D 0.0284 0.6937 0.2779 25 E 0.0279 0.6773 0.2948 26 L 0.0340 0.6040 0.3620 27 F 0.0554 0.4985 0.4462 28 Y 0.0716 0.4264 0.5020 29 C 0.0929 0.3846 0.5225 30 Y 0.0934 0.3323 0.5743 31 P 0.0728 0.3028 0.6245 32 K 0.0642 0.2803 0.6554 33 A 0.0593 0.3125 0.6283 34 I 0.0586 0.3607 0.5808 35 W 0.0577 0.3775 0.5648 36 P 0.0481 0.4332 0.5188 37 F 0.0285 0.6090 0.3625 38 S 0.0147 0.7721 0.2132 39 V 0.0123 0.8345 0.1532 40 A 0.0109 0.8581 0.1310 41 Q 0.0110 0.8688 0.1202 42 L 0.0120 0.8518 0.1362 43 A 0.0144 0.8043 0.1813 44 A 0.0229 0.7051 0.2720 45 A 0.0377 0.5370 0.4253 46 I 0.0438 0.3694 0.5868 47 A 0.0530 0.1932 0.7537 48 E 0.0478 0.1708 0.7814 49 R 0.0803 0.1083 0.8114 50 R 0.2551 0.0411 0.7038 51 G 0.6307 0.0131 0.3562 52 S 0.8802 0.0055 0.1144 53 T 0.9210 0.0034 0.0756 54 V 0.9183 0.0039 0.0779 55 A 0.9125 0.0040 0.0835 56 V 0.8435 0.0102 0.1463 57 H 0.5967 0.0618 0.3415 58 D 0.0633 0.0211 0.9156 59 G 0.0560 0.0326 0.9114 60 Q 0.7334 0.0069 0.2596 61 V 0.9030 0.0030 0.0940 62 L 0.8732 0.0175 0.1093 63 G 0.9135 0.0048 0.0817 64 F 0.9216 0.0042 0.0742 65 A 0.9162 0.0060 0.0778 66 N 0.9174 0.0052 0.0774 67 F 0.8836 0.0089 0.1075 68 Y 0.8372 0.0106 0.1522 69 Q 0.7279 0.0261 0.2460 70 W 0.4112 0.0529 0.5359 71 Q 0.1641 0.0822 0.7537 72 H 0.1035 0.0846 0.8118 73 G 0.0950 0.0880 0.8170 74 D 0.1534 0.0920 0.7546 75 F 0.6006 0.0445 0.3548 76 C 0.8080 0.0179 0.1741 77 A 0.8638 0.0153 0.1209 78 L 0.8751 0.0148 0.1101 79 G 0.7722 0.0491 0.1788 80 N 0.7836 0.0359 0.1805 81 M 0.8244 0.0297 0.1459 82 M 0.8557 0.0163 0.1280 83 V 0.7160 0.0249 0.2591 84 A 0.2508 0.0294 0.7199 85 P 0.0157 0.6674 0.3169 86 A 0.0083 0.7281 0.2636 87 A 0.0152 0.7649 0.2199 88 R 0.0225 0.5655 0.4120 89 G 0.0308 0.3360 0.6332 90 L 0.0584 0.3068 0.6348 91 G 0.0457 0.4370 0.5173 92 V 0.0181 0.8301 0.1518 93 A 0.0068 0.9275 0.0657 94 R 0.0048 0.9566 0.0386 95 Y 0.0047 0.9590 0.0363 96 L 0.0047 0.9586 0.0367 97 I 0.0047 0.9595 0.0358 98 G 0.0048 0.9589 0.0363 99 V 0.0047 0.9583 0.0370 100 M 0.0047 0.9575 0.0377 101 E 0.0047 0.9573 0.0380 102 N 0.0048 0.9535 0.0417 103 L 0.0049 0.9503 0.0448 104 A 0.0051 0.9437 0.0512 105 R 0.0053 0.9171 0.0776 106 E 0.0071 0.8296 0.1633 107 Q 0.0438 0.3223 0.6338 108 Y 0.0402 0.0627 0.8972 109 K 0.0816 0.0839 0.8346 110 A 0.2772 0.1092 0.6136 111 R 0.4548 0.1068 0.4384 112 L 0.7330 0.0461 0.2209 113 M 0.8204 0.0296 0.1500 114 K 0.8486 0.0274 0.1240 115 I 0.8439 0.0367 0.1194 116 S 0.7960 0.0467 0.1574 117 C 0.6671 0.0642 0.2687 118 F 0.4076 0.1049 0.4874 119 N 0.2033 0.1719 0.6248 120 A 0.0690 0.1841 0.7469 121 N 0.0405 0.2593 0.7002 122 A 0.0077 0.8933 0.0990 123 A 0.0053 0.9327 0.0619 124 G 0.0049 0.9515 0.0437 125 L 0.0047 0.9582 0.0371 126 L 0.0047 0.9594 0.0359 127 L 0.0047 0.9593 0.0360 128 Y 0.0050 0.9557 0.0393 129 T 0.0052 0.9463 0.0485 130 Q 0.0060 0.9079 0.0861 131 L 0.0416 0.4829 0.4755 132 G 0.0445 0.0346 0.9208 133 Y 0.1523 0.0210 0.8266 134 Q 0.5066 0.0227 0.4707 135 P 0.5951 0.0401 0.3648 136 R 0.4993 0.0830 0.4177 137 A 0.4038 0.0670 0.5292 138 I 0.4514 0.0787 0.4698 139 A 0.4482 0.0638 0.4880 140 E 0.3630 0.1604 0.4766 141 R 0.2351 0.1698 0.5951 142 H 0.3141 0.1449 0.5410 143 D 0.2491 0.1026 0.6484 144 P 0.1371 0.1182 0.7447 145 D 0.0656 0.1108 0.8236 146 G 0.0483 0.1535 0.7982 147 R 0.0377 0.3640 0.5983 148 R 0.1146 0.4843 0.4011 149 V 0.1502 0.6818 0.1680 150 A 0.1912 0.6974 0.1114 151 L 0.1835 0.7166 0.0999 152 I 0.2081 0.6964 0.0954 153 Q 0.1901 0.6859 0.1240 154 M 0.1942 0.5830 0.2227 155 D 0.1820 0.3898 0.4282 156 K 0.1516 0.1549 0.6935 157 P 0.1153 0.1303 0.7544 158 L 0.0855 0.1033 0.8112 159 E 0.0616 0.0421 0.8963 160 P 0.0448 0.0345 0.9207