# This file is the result of combining several RDB files, specifically # T0346.t06.dssp-ebghstl.rdb (weight 1.53986) # T0346.t06.stride-ebghtl.rdb (weight 1.24869) # T0346.t06.str2.rdb (weight 1.54758) # T0346.t06.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.t06.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.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 88.7316 # # ============================================ # Comments from T0346.t06.stride-ebghtl.rdb # ============================================ # TARGET T0346 # 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 T0346.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 88.7316 # # ============================================ # Comments from T0346.t06.str2.rdb # ============================================ # TARGET T0346 # 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 T0346.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 88.7316 # # ============================================ # Comments from T0346.t06.alpha.rdb # ============================================ # TARGET T0346 # 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 T0346.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 88.7316 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0725 0.0102 0.9173 2 P 0.0871 0.0749 0.8380 3 Q 0.2386 0.0889 0.6725 4 C 0.4909 0.0634 0.4457 5 H 0.5933 0.0410 0.3657 6 F 0.6405 0.0270 0.3324 7 D 0.6742 0.0248 0.3010 8 I 0.7425 0.0342 0.2234 9 E 0.7998 0.0326 0.1676 10 I 0.7669 0.0408 0.1923 11 N 0.5400 0.0331 0.4270 12 R 0.3392 0.0293 0.6315 13 E 0.3446 0.0175 0.6378 14 P 0.3134 0.0330 0.6537 15 V 0.2491 0.0612 0.6897 16 G 0.4584 0.0254 0.5162 17 R 0.7400 0.0072 0.2529 18 I 0.9144 0.0034 0.0822 19 M 0.9277 0.0035 0.0688 20 F 0.9283 0.0033 0.0683 21 Q 0.9091 0.0047 0.0862 22 L 0.7622 0.0192 0.2186 23 F 0.3017 0.0392 0.6590 24 S 0.0667 0.3292 0.6041 25 D 0.0332 0.3839 0.5829 26 I 0.0452 0.4094 0.5453 27 C 0.0472 0.2441 0.7087 28 P 0.0172 0.7131 0.2697 29 K 0.0145 0.8880 0.0975 30 T 0.0146 0.9142 0.0712 31 C 0.0077 0.9447 0.0476 32 K 0.0056 0.9476 0.0468 33 N 0.0053 0.9427 0.0520 34 F 0.0047 0.9520 0.0433 35 L 0.0047 0.9555 0.0398 36 C 0.0051 0.9534 0.0414 37 L 0.0055 0.9424 0.0522 38 C 0.0113 0.8788 0.1099 39 S 0.0445 0.5807 0.3748 40 G 0.0403 0.1664 0.7933 41 E 0.0575 0.1378 0.8046 42 K 0.0991 0.1259 0.7750 43 G 0.1406 0.1139 0.7456 44 L 0.2127 0.1051 0.6822 45 G 0.1988 0.0851 0.7161 46 K 0.1220 0.1826 0.6954 47 T 0.1639 0.1772 0.6589 48 T 0.1535 0.1397 0.7068 49 G 0.1587 0.0775 0.7637 50 K 0.3700 0.0654 0.5646 51 K 0.5337 0.0701 0.3962 52 L 0.5968 0.0921 0.3111 53 C 0.5600 0.0769 0.3631 54 Y 0.4209 0.0984 0.4807 55 K 0.0852 0.0787 0.8361 56 G 0.0533 0.0415 0.9052 57 S 0.3558 0.0262 0.6180 58 T 0.6873 0.0328 0.2799 59 F 0.7310 0.0661 0.2029 60 H 0.7071 0.0799 0.2129 61 R 0.7284 0.0737 0.1980 62 V 0.7410 0.0589 0.2001 63 V 0.6053 0.0623 0.3323 64 K 0.2684 0.1629 0.5687 65 N 0.2249 0.1203 0.6548 66 F 0.5512 0.0725 0.3763 67 M 0.8070 0.0230 0.1700 68 I 0.8206 0.0177 0.1617 69 Q 0.6549 0.0338 0.3113 70 G 0.3402 0.0420 0.6178 71 G 0.1922 0.0419 0.7658 72 D 0.2517 0.0361 0.7123 73 F 0.1485 0.1300 0.7215 74 S 0.1347 0.1269 0.7383 75 E 0.1211 0.1043 0.7746 76 G 0.1013 0.0576 0.8411 77 N 0.1208 0.0437 0.8355 78 G 0.1214 0.0542 0.8244 79 K 0.2020 0.0617 0.7363 80 G 0.1676 0.0509 0.7815 81 G 0.1973 0.0441 0.7586 82 E 0.3467 0.0569 0.5964 83 S 0.3640 0.0663 0.5697 84 I 0.3458 0.1065 0.5477 85 Y 0.2143 0.0944 0.6913 86 G 0.0939 0.0605 0.8456 87 G 0.1675 0.0476 0.7848 88 Y 0.3492 0.0498 0.6010 89 F 0.2549 0.0804 0.6647 90 K 0.1702 0.1535 0.6763 91 D 0.1436 0.1739 0.6825 92 E 0.1348 0.2858 0.5794 93 N 0.1589 0.2297 0.6114 94 F 0.2061 0.1945 0.5994 95 I 0.2770 0.1886 0.5344 96 L 0.3359 0.1612 0.5029 97 K 0.2628 0.1647 0.5725 98 H 0.2125 0.1387 0.6488 99 D 0.1374 0.0836 0.7791 100 R 0.1399 0.1484 0.7118 101 A 0.2415 0.1610 0.5975 102 F 0.5022 0.1388 0.3590 103 L 0.7215 0.1259 0.1526 104 L 0.7437 0.1437 0.1126 105 S 0.6975 0.1627 0.1398 106 M 0.6277 0.1852 0.1871 107 A 0.5212 0.2089 0.2699 108 N 0.3453 0.1896 0.4651 109 R 0.1922 0.1239 0.6839 110 G 0.0877 0.0353 0.8771 111 K 0.0580 0.0754 0.8666 112 H 0.0694 0.0603 0.8703 113 T 0.1225 0.0666 0.8109 114 N 0.1128 0.0603 0.8269 115 G 0.1332 0.0629 0.8039 116 S 0.2956 0.0422 0.6622 117 Q 0.6054 0.0340 0.3606 118 F 0.8309 0.0207 0.1484 119 F 0.8917 0.0163 0.0920 120 I 0.8959 0.0147 0.0894 121 T 0.8479 0.0127 0.1394 122 T 0.5973 0.0251 0.3776 123 K 0.2815 0.0241 0.6944 124 P 0.2003 0.0330 0.7667 125 A 0.1099 0.0678 0.8224 126 P 0.0537 0.2786 0.6677 127 H 0.0572 0.2917 0.6511 128 L 0.1416 0.1590 0.6994 129 D 0.0633 0.0747 0.8620 130 G 0.0686 0.0583 0.8731 131 V 0.2793 0.0431 0.6776 132 H 0.6913 0.0126 0.2961 133 V 0.7871 0.0097 0.2033 134 V 0.8436 0.0139 0.1425 135 F 0.7238 0.0358 0.2404 136 G 0.6587 0.0325 0.3088 137 L 0.7766 0.0366 0.1868 138 V 0.7922 0.0474 0.1604 139 I 0.5320 0.1376 0.3304 140 S 0.2281 0.1874 0.5845 141 G 0.0464 0.4398 0.5138 142 F 0.0183 0.8231 0.1587 143 E 0.0190 0.8889 0.0921 144 V 0.0102 0.9329 0.0569 145 I 0.0080 0.9411 0.0509 146 E 0.0079 0.9404 0.0517 147 Q 0.0082 0.9251 0.0667 148 I 0.0142 0.8671 0.1187 149 E 0.0134 0.7519 0.2347 150 N 0.0204 0.5293 0.4503 151 L 0.0836 0.1611 0.7553 152 K 0.1280 0.0642 0.8078 153 T 0.2452 0.0559 0.6990 154 D 0.1267 0.0614 0.8120 155 A 0.0352 0.2504 0.7144 156 A 0.0417 0.1294 0.8288 157 S 0.0563 0.0667 0.8769 158 R 0.1582 0.0138 0.8279 159 P 0.3169 0.0147 0.6683 160 Y 0.3281 0.0445 0.6274 161 A 0.3843 0.0538 0.5619 162 D 0.4594 0.0201 0.5204 163 V 0.6393 0.0068 0.3538 164 R 0.8455 0.0054 0.1491 165 V 0.8938 0.0041 0.1021 166 I 0.8317 0.0286 0.1397 167 D 0.7686 0.0143 0.2171 168 C 0.6791 0.0338 0.2871 169 G 0.6955 0.0348 0.2697 170 V 0.6910 0.0317 0.2773 171 L 0.3336 0.0427 0.6236 172 A 0.0754 0.0212 0.9034