# This file is the result of combining several RDB files, specifically # T0419.t06.str2.rdb (weight 1.54425) # T0419.t06.str4.rdb (weight 0.924988) # T0419.t06.pb.rdb (weight 0.789901) # T0419.t06.bys.rdb (weight 0.748322) # T0419.t06.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 T0419.t06.str2.rdb # ============================================ # TARGET T0419 # Using neural net dunbrack-40pc-3157-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 T0419.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 4.29063 # # ============================================ # Comments from T0419.t06.str4.rdb # ============================================ # TARGET T0419 # Using neural net dunbrack-40pc-3157-t06-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 T0419.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 4.29063 # # ============================================ # Comments from T0419.t06.pb.rdb # ============================================ # TARGET T0419 # Using neural net dunbrack-40pc-3157-t06-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 T0419.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 4.29063 # # ============================================ # Comments from T0419.t06.bys.rdb # ============================================ # TARGET T0419 # Using neural net dunbrack-40pc-3157-t06-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 T0419.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 4.29063 # # ============================================ # Comments from T0419.t06.alpha.rdb # ============================================ # TARGET T0419 # Using neural net dunbrack-40pc-3157-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 T0419.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 4.29063 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 K 0.1861 0.1391 0.6748 2 E 0.1728 0.1865 0.6408 3 R 0.2021 0.2462 0.5517 4 A 0.2173 0.2751 0.5075 5 K 0.2797 0.2066 0.5138 6 R 0.3125 0.1273 0.5601 7 Q 0.2851 0.0551 0.6598 8 P 0.2142 0.1359 0.6500 9 H 0.2239 0.1599 0.6162 10 A 0.2602 0.1358 0.6040 11 A 0.2799 0.0952 0.6248 12 P 0.2853 0.1590 0.5557 13 L 0.2964 0.2277 0.4759 14 V 0.3417 0.2275 0.4309 15 S 0.3234 0.2072 0.4694 16 S 0.2393 0.2018 0.5589 17 L 0.1341 0.3332 0.5327 18 D 0.1195 0.3242 0.5563 19 N 0.0662 0.4615 0.4723 20 R 0.0760 0.5406 0.3834 21 G 0.0723 0.5653 0.3624 22 L 0.0908 0.5636 0.3455 23 L 0.0987 0.5914 0.3098 24 D 0.0739 0.5861 0.3401 25 S 0.0841 0.6020 0.3138 26 L 0.1142 0.5408 0.3450 27 D 0.1260 0.5011 0.3729 28 L 0.0513 0.6718 0.2769 29 G 0.0425 0.6936 0.2640 30 Q 0.0377 0.7182 0.2441 31 Y 0.0619 0.6062 0.3319 32 L 0.1322 0.3897 0.4781 33 D 0.1202 0.2161 0.6637 34 K 0.0267 0.6959 0.2774 35 D 0.0175 0.8047 0.1778 36 A 0.0142 0.8674 0.1183 37 Y 0.0157 0.8915 0.0928 38 K 0.0089 0.9154 0.0757 39 E 0.0083 0.9203 0.0714 40 Q 0.0084 0.9192 0.0725 41 L 0.0087 0.9188 0.0725 42 A 0.0084 0.9189 0.0727 43 A 0.0083 0.9205 0.0711 44 E 0.0083 0.9212 0.0705 45 Q 0.0084 0.9181 0.0735 46 A 0.0086 0.9175 0.0739 47 R 0.0091 0.9158 0.0751 48 L 0.0102 0.8863 0.1035 49 A 0.0218 0.7912 0.1870 50 G 0.0189 0.7488 0.2324 51 L 0.0278 0.7971 0.1751 52 I 0.0545 0.7310 0.2145 53 R 0.0693 0.6576 0.2731 54 D 0.0847 0.6104 0.3048 55 K 0.0247 0.7438 0.2314 56 R 0.0361 0.6921 0.2718 57 F 0.0894 0.5858 0.3248 58 R 0.1266 0.4709 0.4025 59 Q 0.1574 0.3295 0.5131 60 H 0.1681 0.1971 0.6349