# This file is the result of combining several RDB files, specifically # T0498.t06.str2.rdb (weight 1.54425) # T0498.t06.str4.rdb (weight 0.924988) # T0498.t06.pb.rdb (weight 0.789901) # T0498.t06.bys.rdb (weight 0.748322) # T0498.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 T0498.t06.str2.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t06.str4.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t06.pb.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t06.bys.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t06.alpha.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.4757 0.0554 0.4689 2 T 0.5958 0.0315 0.3728 3 Y 0.7401 0.0178 0.2421 4 K 0.7903 0.0122 0.1974 5 L 0.8080 0.0070 0.1850 6 I 0.8038 0.0078 0.1884 7 L 0.7719 0.0119 0.2162 8 N 0.5727 0.0347 0.3926 9 L 0.2805 0.1698 0.5497 10 K 0.2066 0.3390 0.4544 11 Q 0.2061 0.3921 0.4018 12 A 0.1499 0.4436 0.4065 13 K 0.0874 0.5667 0.3459 14 E 0.0513 0.7242 0.2245 15 E 0.0489 0.7904 0.1608 16 A 0.0454 0.8063 0.1483 17 I 0.0359 0.8365 0.1276 18 K 0.0337 0.8305 0.1358 19 E 0.0396 0.8135 0.1469 20 L 0.0642 0.7261 0.2097 21 V 0.1524 0.5794 0.2682 22 D 0.1439 0.4575 0.3986 23 A 0.0182 0.7535 0.2283 24 G 0.0112 0.8322 0.1566 25 T 0.0115 0.8827 0.1058 26 A 0.0091 0.8999 0.0909 27 E 0.0084 0.9138 0.0778 28 K 0.0083 0.9215 0.0702 29 Y 0.0083 0.9224 0.0693 30 I 0.0083 0.9208 0.0709 31 K 0.0084 0.9191 0.0725 32 L 0.0093 0.9068 0.0839 33 I 0.0171 0.8549 0.1280 34 A 0.0341 0.7588 0.2071 35 N 0.0562 0.6122 0.3315 36 A 0.0528 0.4199 0.5273 37 K 0.0783 0.2513 0.6704 38 T 0.1770 0.1416 0.6813 39 V 0.3438 0.0877 0.5685 40 E 0.3261 0.0763 0.5977 41 G 0.4010 0.0554 0.5436 42 V 0.5346 0.0581 0.4073 43 W 0.6674 0.0393 0.2933 44 T 0.6019 0.0454 0.3527 45 L 0.4442 0.1288 0.4270 46 K 0.2494 0.2924 0.4582 47 D 0.1979 0.3641 0.4381 48 E 0.2609 0.2876 0.4515 49 I 0.4203 0.1439 0.4358 50 K 0.5666 0.0777 0.3558 51 T 0.6632 0.0312 0.3055 52 F 0.6990 0.0206 0.2804 53 T 0.6888 0.0156 0.2955 54 V 0.5758 0.0302 0.3940 55 T 0.4346 0.0453 0.5201 56 E 0.3200 0.1180 0.5620