# This file is the result of combining several RDB files, specifically # T0472.t06.str2.rdb (weight 1.54425) # T0472.t06.str4.rdb (weight 0.924988) # T0472.t06.pb.rdb (weight 0.789901) # T0472.t06.bys.rdb (weight 0.748322) # T0472.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 T0472.t06.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ # Comments from T0472.t06.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ # Comments from T0472.t06.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ # Comments from T0472.t06.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ # Comments from T0472.t06.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.1843 0.2341 0.5816 2 I 0.1274 0.5118 0.3608 3 E 0.1258 0.5829 0.2913 4 A 0.1883 0.5336 0.2782 5 R 0.2842 0.4283 0.2875 6 Y 0.4055 0.3311 0.2634 7 A 0.4722 0.2888 0.2390 8 K 0.5144 0.2708 0.2148 9 E 0.5174 0.2551 0.2275 10 V 0.5091 0.2303 0.2606 11 A 0.3406 0.2749 0.3845 12 K 0.1310 0.3205 0.5485 13 N 0.0951 0.1497 0.7552 14 D 0.0777 0.0795 0.8428 15 K 0.3968 0.0178 0.5854 16 P 0.6183 0.0167 0.3650 17 Y 0.7734 0.0107 0.2159 18 F 0.8146 0.0058 0.1796 19 N 0.7863 0.0067 0.2069 20 L 0.7801 0.0131 0.2068 21 K 0.7522 0.0247 0.2231 22 A 0.6504 0.0507 0.2990 23 A 0.3743 0.1534 0.4724 24 N 0.1700 0.1074 0.7226 25 H 0.1932 0.0899 0.7170 26 Q 0.5196 0.0385 0.4419 27 I 0.6921 0.0227 0.2853 28 I 0.6841 0.0388 0.2771 29 G 0.6413 0.0514 0.3073 30 T 0.5164 0.0971 0.3864 31 S 0.3631 0.1196 0.5173 32 Q 0.2072 0.2962 0.4966 33 M 0.1829 0.3684 0.4487 34 Y 0.2235 0.3353 0.4412 35 S 0.2101 0.3264 0.4636 36 S 0.1335 0.4046 0.4619 37 T 0.0257 0.7297 0.2446 38 A 0.0215 0.8166 0.1619 39 A 0.0250 0.8320 0.1430 40 R 0.0225 0.8473 0.1302 41 D 0.0218 0.7799 0.1983 42 N 0.0333 0.6352 0.3315 43 G 0.0434 0.6756 0.2810 44 I 0.0515 0.7592 0.1892 45 K 0.0407 0.7952 0.1641 46 S 0.0539 0.8099 0.1362 47 V 0.0836 0.7583 0.1580 48 M 0.1069 0.6789 0.2142 49 E 0.0959 0.5051 0.3990 50 N 0.0815 0.2476 0.6708 51 G 0.1281 0.1132 0.7587 52 K 0.1196 0.2008 0.6796 53 T 0.1497 0.1660 0.6842 54 T 0.2375 0.1541 0.6084 55 T 0.3182 0.1644 0.5174 56 I 0.3983 0.2380 0.3637 57 K 0.3502 0.2705 0.3793 58 D 0.3316 0.2331 0.4352 59 L 0.2649 0.2082 0.5269 60 T 0.2273 0.1461 0.6266