# This file is the result of combining several RDB files, specifically # T0499.t04.str2.rdb (weight 1.54425) # T0499.t04.str4.rdb (weight 0.924988) # T0499.t04.pb.rdb (weight 0.789901) # T0499.t04.bys.rdb (weight 0.748322) # T0499.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 T0499.t04.str2.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.77849 # # ============================================ # Comments from T0499.t04.str4.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.77849 # # ============================================ # Comments from T0499.t04.pb.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.77849 # # ============================================ # Comments from T0499.t04.bys.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.77849 # # ============================================ # Comments from T0499.t04.alpha.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.77849 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.3659 0.0735 0.5606 2 T 0.5301 0.0506 0.4193 3 Y 0.7004 0.0272 0.2724 4 K 0.7746 0.0169 0.2084 5 L 0.8089 0.0090 0.1820 6 I 0.8134 0.0090 0.1776 7 L 0.7813 0.0119 0.2067 8 N 0.6366 0.0274 0.3360 9 L 0.3475 0.1744 0.4781 10 K 0.1842 0.3179 0.4979 11 Q 0.1589 0.3675 0.4736 12 A 0.1479 0.4267 0.4254 13 K 0.1086 0.5567 0.3347 14 E 0.0580 0.7367 0.2054 15 E 0.0651 0.7657 0.1691 16 A 0.0788 0.7546 0.1666 17 I 0.0673 0.7530 0.1797 18 K 0.0569 0.7578 0.1853 19 E 0.0532 0.7599 0.1870 20 A 0.0588 0.7592 0.1819 21 V 0.1362 0.6005 0.2633 22 D 0.1017 0.5268 0.3715 23 A 0.0236 0.7444 0.2320 24 G 0.0163 0.8362 0.1475 25 T 0.0175 0.8802 0.1022 26 A 0.0095 0.9050 0.0854 27 E 0.0085 0.9178 0.0736 28 K 0.0084 0.9208 0.0709 29 Y 0.0089 0.9165 0.0746 30 F 0.0089 0.9112 0.0799 31 K 0.0086 0.9174 0.0741 32 L 0.0102 0.9132 0.0765 33 I 0.0164 0.8767 0.1069 34 A 0.0391 0.7730 0.1880 35 N 0.0560 0.5368 0.4072 36 A 0.0599 0.3831 0.5570 37 K 0.0873 0.1910 0.7217 38 T 0.1579 0.1074 0.7347 39 V 0.3291 0.0646 0.6063 40 E 0.2909 0.0904 0.6187 41 G 0.3970 0.0527 0.5503 42 V 0.5268 0.0508 0.4224 43 W 0.6287 0.0348 0.3365 44 T 0.5698 0.0401 0.3901 45 Y 0.4367 0.0931 0.4702 46 K 0.2596 0.2443 0.4961 47 D 0.1867 0.3206 0.4927 48 E 0.2691 0.2734 0.4574 49 I 0.4346 0.1424 0.4230 50 K 0.5966 0.0943 0.3091 51 T 0.6720 0.0332 0.2948 52 F 0.6797 0.0251 0.2952 53 T 0.6762 0.0196 0.3042 54 V 0.5943 0.0390 0.3667 55 T 0.4314 0.0575 0.5111 56 E 0.3116 0.1473 0.5411