# This file is the result of combining several RDB files, specifically # T0357.t06.dssp-ebghstl.rdb (weight 1.53986) # T0357.t06.stride-ebghtl.rdb (weight 1.24869) # T0357.t06.str2.rdb (weight 1.54758) # T0357.t06.alpha.rdb (weight 0.659012) # 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 T0357.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0357 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0357.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 3.34133 # # ============================================ # Comments from T0357.t06.stride-ebghtl.rdb # ============================================ # TARGET T0357 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0357.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 3.34133 # # ============================================ # Comments from T0357.t06.str2.rdb # ============================================ # TARGET T0357 # Using neural net 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 T0357.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 3.34133 # # ============================================ # Comments from T0357.t06.alpha.rdb # ============================================ # TARGET T0357 # Using neural net 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 T0357.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 3.34133 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0789 0.0332 0.8878 2 K 0.2891 0.0754 0.6355 3 A 0.6811 0.0552 0.2637 4 I 0.8194 0.0419 0.1387 5 I 0.7938 0.0460 0.1602 6 N 0.5871 0.0388 0.3741 7 K 0.1610 0.1749 0.6641 8 K 0.0773 0.1387 0.7840 9 T 0.1099 0.1192 0.7709 10 E 0.1639 0.1228 0.7132 11 T 0.3250 0.1624 0.5125 12 I 0.6148 0.2038 0.1814 13 I 0.6752 0.1791 0.1457 14 A 0.6728 0.1852 0.1419 15 V 0.4880 0.3244 0.1876 16 G 0.3572 0.3276 0.3152 17 A 0.3639 0.3744 0.2617 18 A 0.3804 0.3807 0.2389 19 M 0.3206 0.4109 0.2685 20 A 0.2021 0.2981 0.4998 21 E 0.1475 0.2301 0.6224 22 I 0.2053 0.0301 0.7646 23 P 0.1971 0.0386 0.7642 24 L 0.4038 0.1984 0.3979 25 V 0.4489 0.2449 0.3062 26 E 0.4660 0.2383 0.2957 27 V 0.3100 0.3015 0.3886 28 R 0.2201 0.2385 0.5414 29 D 0.1226 0.2150 0.6624 30 E 0.0461 0.5660 0.3879 31 K 0.0921 0.5762 0.3317 32 F 0.0877 0.7162 0.1961 33 F 0.1460 0.6740 0.1800 34 E 0.1745 0.6771 0.1485 35 A 0.1926 0.6727 0.1347 36 V 0.2191 0.5125 0.2684 37 K 0.1716 0.3388 0.4896 38 T 0.0627 0.0917 0.8456 39 G 0.0497 0.0289 0.9214 40 D 0.1791 0.0251 0.7959 41 R 0.8091 0.0055 0.1855 42 V 0.9037 0.0036 0.0928 43 V 0.9175 0.0034 0.0791 44 V 0.8745 0.0055 0.1200 45 N 0.5960 0.0071 0.3969 46 A 0.0993 0.0950 0.8056 47 D 0.0546 0.1058 0.8396 48 E 0.0767 0.0873 0.8360 49 G 0.2018 0.0448 0.7534 50 Y 0.7504 0.0174 0.2322 51 V 0.8806 0.0075 0.1119 52 E 0.8763 0.0088 0.1149 53 L 0.8260 0.0127 0.1613 54 I 0.4138 0.0334 0.5529 55 E 0.1094 0.0254 0.8652