# This file is the result of combining several RDB files, specifically # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.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 T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 12.5126 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 12.5126 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 12.5126 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 12.5126 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1113 0.0587 0.8300 2 Y 0.5243 0.0354 0.4403 3 V 0.6979 0.0290 0.2731 4 A 0.6876 0.0237 0.2887 5 T 0.5850 0.0491 0.3659 6 G 0.4801 0.0720 0.4479 7 H 0.5608 0.1006 0.3386 8 Y 0.7356 0.0621 0.2023 9 A 0.8189 0.0317 0.1494 10 R 0.8575 0.0234 0.1191 11 V 0.8673 0.0205 0.1122 12 A 0.8467 0.0158 0.1375 13 R 0.7526 0.0266 0.2208 14 D 0.3087 0.0384 0.6529 15 E 0.0615 0.1160 0.8225 16 D 0.0510 0.0280 0.9210 17 G 0.0918 0.0299 0.8783 18 T 0.4352 0.0186 0.5461 19 V 0.8553 0.0061 0.1386 20 H 0.8781 0.0099 0.1120 21 M 0.8960 0.0095 0.0945 22 L 0.8593 0.0165 0.1242 23 R 0.7404 0.0317 0.2279 24 G 0.5215 0.0440 0.4345 25 V 0.3747 0.0623 0.5631 26 D 0.1793 0.0514 0.7693 27 N 0.0399 0.1107 0.8494 28 G 0.0318 0.1026 0.8656 29 K 0.0810 0.1580 0.7610 30 D 0.1481 0.1608 0.6911 31 Q 0.2550 0.4121 0.3328 32 T 0.3505 0.4809 0.1686 33 Y 0.3597 0.5272 0.1132 34 F 0.3148 0.5656 0.1196 35 L 0.2859 0.5346 0.1795 36 S 0.1558 0.4769 0.3673 37 Q 0.1171 0.3008 0.5821 38 L 0.1127 0.0786 0.8087 39 S 0.0649 0.0384 0.8968 40 Q 0.0049 0.9355 0.0597 41 E 0.0047 0.9496 0.0457 42 Q 0.0048 0.9493 0.0458 43 L 0.0051 0.9418 0.0531 44 Q 0.0057 0.8929 0.1013 45 K 0.0114 0.7322 0.2564 46 T 0.0341 0.5856 0.3802 47 M 0.1231 0.2424 0.6346 48 F 0.1300 0.0688 0.8012 49 P 0.1171 0.0967 0.7862 50 L 0.0658 0.2915 0.6427 51 G 0.0432 0.2693 0.6875 52 H 0.0553 0.2460 0.6987 53 L 0.0842 0.1112 0.8046 54 E 0.0691 0.0702 0.8607 55 K 0.0292 0.6768 0.2940 56 P 0.0057 0.9405 0.0537 57 E 0.0048 0.9548 0.0404 58 V 0.0050 0.9571 0.0379 59 R 0.0047 0.9607 0.0347 60 R 0.0046 0.9613 0.0341 61 L 0.0046 0.9617 0.0336 62 A 0.0047 0.9610 0.0344 63 E 0.0048 0.9555 0.0397 64 E 0.0052 0.9336 0.0612 65 A 0.0426 0.4819 0.4755 66 G 0.0440 0.0247 0.9313 67 L 0.0717 0.0178 0.9105 68 S 0.1149 0.0849 0.8002 69 T 0.2099 0.1924 0.5977 70 A 0.1917 0.1785 0.6298 71 K 0.1867 0.1464 0.6669 72 K 0.1334 0.1401 0.7265 73 K 0.0862 0.2203 0.6936 74 D 0.0820 0.2062 0.7117 75 S 0.1825 0.1115 0.7060 76 T 0.1836 0.0841 0.7324 77 G 0.3431 0.0490 0.6080 78 I 0.7685 0.0150 0.2165 79 C 0.8656 0.0091 0.1254 80 F 0.8289 0.0102 0.1609 81 I 0.5503 0.0293 0.4204 82 G 0.1877 0.0331 0.7792 83 E 0.0861 0.1301 0.7838 84 K 0.0554 0.2538 0.6908 85 N 0.0854 0.2639 0.6507 86 F 0.0107 0.8685 0.1209 87 K 0.0059 0.9358 0.0583 88 N 0.0054 0.9431 0.0516 89 F 0.0055 0.9452 0.0493 90 L 0.0065 0.9303 0.0632 91 S 0.0072 0.8894 0.1034 92 N 0.0110 0.7607 0.2283 93 Y 0.0269 0.5273 0.4458 94 L 0.0807 0.0765 0.8428 95 P 0.0769 0.0654 0.8577 96 A 0.1142 0.0458 0.8400 97 Q 0.0981 0.0208 0.8811 98 P 0.0691 0.0635 0.8674 99 G 0.1186 0.0409 0.8404 100 R 0.4845 0.0238 0.4917 101 M 0.8261 0.0084 0.1654 102 M 0.8579 0.0073 0.1348 103 T 0.7144 0.0082 0.2774 104 V 0.3004 0.0951 0.6045 105 D 0.0668 0.0408 0.8924 106 G 0.0853 0.0404 0.8743 107 R 0.4192 0.0225 0.5583 108 D 0.7921 0.0153 0.1926 109 M 0.6983 0.0487 0.2530 110 G 0.5983 0.0519 0.3498 111 E 0.5400 0.0665 0.3935 112 H 0.4421 0.0628 0.4952 113 A 0.2430 0.0830 0.6740 114 G 0.2829 0.0442 0.6729 115 L 0.5836 0.0408 0.3757 116 M 0.8023 0.0242 0.1735 117 Y 0.8306 0.0289 0.1405 118 Y 0.7846 0.0414 0.1740 119 T 0.6485 0.0696 0.2819 120 I 0.4498 0.1901 0.3601 121 G 0.3081 0.2187 0.4732 122 Q 0.2714 0.2733 0.4553 123 R 0.2319 0.2939 0.4742 124 G 0.1500 0.1915 0.6585 125 G 0.1650 0.1211 0.7140 126 L 0.2759 0.0796 0.6444 127 G 0.3126 0.0589 0.6285 128 I 0.3092 0.0879 0.6030 129 G 0.2446 0.0841 0.6713 130 G 0.2022 0.0870 0.7108 131 Q 0.1951 0.0788 0.7261 132 H 0.1548 0.0757 0.7694 133 G 0.0779 0.0643 0.8578 134 G 0.0582 0.0722 0.8695 135 D 0.0817 0.0691 0.8492 136 N 0.0921 0.0504 0.8575 137 A 0.1572 0.0171 0.8258 138 P 0.3308 0.0193 0.6500 139 W 0.7458 0.0148 0.2394 140 F 0.8989 0.0062 0.0949 141 V 0.9079 0.0054 0.0867 142 V 0.8133 0.0271 0.1596 143 G 0.6104 0.0247 0.3650 144 K 0.3849 0.0468 0.5683 145 D 0.2624 0.0389 0.6987 146 L 0.0754 0.2262 0.6985 147 S 0.0459 0.1858 0.7682 148 K 0.0435 0.0946 0.8618