# This file is the result of combining several RDB files, specifically # T0344.t06.dssp-ebghstl.rdb (weight 1.53986) # T0344.t06.stride-ebghtl.rdb (weight 1.24869) # T0344.t06.str2.rdb (weight 1.54758) # T0344.t06.alpha.rdb (weight 0.659012) # T0344.t04.dssp-ebghstl.rdb (weight 1.53986) # T0344.t04.stride-ebghtl.rdb (weight 1.24869) # T0344.t04.str2.rdb (weight 1.54758) # T0344.t04.alpha.rdb (weight 0.659012) # T0344.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0344.t2k.stride-ebghtl.rdb (weight 1.24869) # T0344.t2k.str2.rdb (weight 1.54758) # T0344.t2k.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 T0344.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t06.stride-ebghtl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t06.str2.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t06.alpha.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # 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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t04.stride-ebghtl.rdb # ============================================ # TARGET T0344 # Using neural net t04-2621-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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t04.str2.rdb # ============================================ # TARGET T0344 # Using neural net t04-2621-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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t04.alpha.rdb # ============================================ # TARGET T0344 # Using neural net t04-2621-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 T0344.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 2.37146 # # ============================================ # Comments from T0344.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0344 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0344.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 4 # # ============================================ # Comments from T0344.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0344 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0344.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 4 # # ============================================ # Comments from T0344.t2k.str2.rdb # ============================================ # TARGET T0344 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0344.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 4 # # ============================================ # Comments from T0344.t2k.alpha.rdb # ============================================ # TARGET T0344 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0344.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 4 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.2887 0.0275 0.6838 2 I 0.5743 0.0251 0.4006 3 I 0.5586 0.0344 0.4071 4 G 0.3548 0.0247 0.6205 5 L 0.1924 0.0232 0.7844 6 P 0.1538 0.0593 0.7869 7 R 0.2100 0.1016 0.6884 8 Y 0.5220 0.0577 0.4204 9 M 0.6369 0.0187 0.3444 10 E 0.8248 0.0065 0.1687 11 V 0.8436 0.0055 0.1509 12 N 0.8281 0.0037 0.1682 13 I 0.6724 0.0073 0.3203 14 K 0.4096 0.0178 0.5725 15 D 0.0607 0.0504 0.8889 16 G 0.0441 0.0418 0.9141 17 K 0.4455 0.0171 0.5374 18 I 0.7518 0.0099 0.2382 19 I 0.6679 0.0357 0.2963 20 G 0.4602 0.0330 0.5067 21 R 0.3497 0.0378 0.6125 22 S 0.3764 0.0350 0.5886 23 L 0.2829 0.0299 0.6872 24 D 0.1801 0.0214 0.7985 25 P 0.0550 0.3034 0.6416 26 R 0.0427 0.2651 0.6921 27 E 0.1122 0.2634 0.6244 28 G 0.1497 0.1262 0.7240 29 G 0.1971 0.0916 0.7113 30 L 0.3899 0.0756 0.5345 31 Y 0.6224 0.0432 0.3344 32 G 0.7069 0.0224 0.2706 33 S 0.8402 0.0089 0.1509 34 A 0.8637 0.0082 0.1281 35 E 0.8923 0.0045 0.1032 36 V 0.8502 0.0062 0.1436 37 S 0.8094 0.0087 0.1819 38 V 0.4891 0.0179 0.4930 39 P 0.1404 0.0638 0.7958 40 E 0.0489 0.0694 0.8817 41 G 0.0977 0.0489 0.8534 42 V 0.3842 0.0094 0.6064 43 K 0.7572 0.0086 0.2342 44 W 0.8653 0.0063 0.1284 45 E 0.8666 0.0079 0.1255 46 I 0.7915 0.0158 0.1927 47 Y 0.4264 0.0148 0.5588 48 P 0.1669 0.0287 0.8044 49 N 0.0904 0.0242 0.8854 50 P 0.0398 0.4049 0.5553 51 V 0.1057 0.4615 0.4328 52 A 0.1951 0.4699 0.3351 53 R 0.3098 0.3829 0.3072 54 R 0.4070 0.3061 0.2869 55 F 0.5106 0.2277 0.2617 56 M 0.6988 0.0989 0.2023 57 I 0.7992 0.0748 0.1261 58 F 0.8253 0.0496 0.1251 59 E 0.8343 0.0296 0.1361 60 I 0.7310 0.0544 0.2146 61 F 0.5231 0.0662 0.4107 62 S 0.3249 0.0667 0.6084 63 K 0.1428 0.0720 0.7852 64 R 0.0417 0.0370 0.9212