# This file is the result of combining several RDB files, specifically # TR453.t04.str2.rdb (weight 1.54425) # TR453.t04.str4.rdb (weight 0.924988) # TR453.t04.pb.rdb (weight 0.789901) # TR453.t04.bys.rdb (weight 0.748322) # TR453.t04.alpha.rdb (weight 0.678173) # 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 TR453.t04.str2.rdb # ============================================ # TARGET TR453 # Using neural net dunbrack-40pc-3157-t04-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 TR453.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 130.223 # # ============================================ # Comments from TR453.t04.str4.rdb # ============================================ # TARGET TR453 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment TR453.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 130.223 # # ============================================ # Comments from TR453.t04.pb.rdb # ============================================ # TARGET TR453 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment TR453.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 130.223 # # ============================================ # Comments from TR453.t04.bys.rdb # ============================================ # TARGET TR453 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment TR453.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 130.223 # # ============================================ # Comments from TR453.t04.alpha.rdb # ============================================ # TARGET TR453 # Using neural net dunbrack-40pc-3157-t04-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 TR453.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 130.223 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.2019 0.1534 0.6447 2 E 0.3383 0.1571 0.5046 3 I 0.5878 0.0643 0.3479 4 V 0.6787 0.0348 0.2865 5 Q 0.6720 0.0247 0.3032 6 R 0.4716 0.0514 0.4770 7 E 0.2753 0.1533 0.5714 8 D 0.1087 0.1439 0.7473 9 G 0.0974 0.0946 0.8080 10 S 0.5141 0.0188 0.4671 11 W 0.7164 0.0123 0.2713 12 L 0.7858 0.0111 0.2031 13 V 0.7757 0.0127 0.2116 14 D 0.6468 0.0367 0.3165 15 G 0.5966 0.0596 0.3438 16 M 0.5444 0.0634 0.3922 17 V 0.4676 0.0314 0.5010 18 S 0.2558 0.0186 0.7257 19 L 0.0263 0.6976 0.2761 20 D 0.0104 0.8499 0.1397 21 R 0.0099 0.9012 0.0888 22 F 0.0092 0.8952 0.0955 23 R 0.0097 0.8962 0.0941 24 E 0.0101 0.8664 0.1235 25 F 0.0218 0.7696 0.2086 26 F 0.0716 0.4390 0.4894 27 E 0.0685 0.2872 0.6443 28 L 0.1965 0.1427 0.6607 29 E 0.2337 0.0975 0.6687 30 A 0.3020 0.0476 0.6504 31 P 0.2234 0.0516 0.7250 32 L 0.2302 0.0773 0.6925 33 P 0.1667 0.1274 0.7059 34 G 0.1228 0.1541 0.7230 35 E 0.1917 0.1676 0.6406 36 A 0.1640 0.2183 0.6176 37 G 0.1076 0.1618 0.7307 38 G 0.1067 0.1602 0.7330 39 N 0.2502 0.1391 0.6106 40 I 0.3424 0.2043 0.4533 41 H 0.2798 0.3491 0.3711 42 T 0.2098 0.5351 0.2552 43 L 0.1150 0.6717 0.2134 44 A 0.0547 0.7938 0.1515 45 G 0.0370 0.8605 0.1025 46 V 0.0370 0.8790 0.0839 47 M 0.0364 0.8826 0.0809 48 L 0.0289 0.8828 0.0882 49 Y 0.0250 0.8733 0.1017 50 Q 0.0290 0.7798 0.1913 51 L 0.0709 0.4296 0.4995 52 G 0.0674 0.1623 0.7703 53 R 0.1732 0.0988 0.7280 54 V 0.2536 0.0234 0.7230 55 P 0.2184 0.0418 0.7399 56 S 0.2055 0.0769 0.7176 57 V 0.1852 0.2048 0.6100 58 T 0.1926 0.1555 0.6519 59 D 0.4446 0.0600 0.4955 60 R 0.7207 0.0135 0.2659 61 F 0.7578 0.0103 0.2319 62 E 0.7361 0.0083 0.2556 63 W 0.6562 0.0328 0.3110 64 N 0.2566 0.0626 0.6808 65 G 0.1812 0.0543 0.7645 66 F 0.5602 0.0129 0.4269 67 S 0.7352 0.0089 0.2560 68 F 0.8114 0.0046 0.1839 69 E 0.8020 0.0060 0.1920 70 V 0.7431 0.0052 0.2518 71 V 0.7539 0.0155 0.2307 72 D 0.6998 0.0144 0.2858 73 M 0.5532 0.0747 0.3722 74 D 0.2962 0.1005 0.6033 75 R 0.1602 0.1947 0.6452 76 T 0.2691 0.1243 0.6066 77 R 0.5305 0.0524 0.4171 78 V 0.6408 0.0142 0.3449 79 D 0.5699 0.0633 0.3668 80 K 0.7955 0.0066 0.1979 81 I 0.7705 0.0064 0.2231 82 L 0.7954 0.0059 0.1988 83 V 0.7835 0.0075 0.2090 84 Q 0.6384 0.0158 0.3458 85 R 0.4312 0.0454 0.5234 86 H 0.2419 0.0836 0.6745 87 H 0.2135 0.1074 0.6791