# This file is the result of combining several RDB files, specifically # T0357.t04.dssp-ebghstl.rdb (weight 1.53986) # T0357.t04.stride-ebghtl.rdb (weight 1.24869) # T0357.t04.str2.rdb (weight 1.54758) # T0357.t04.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.t04.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.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 3.34133 # # ============================================ # Comments from T0357.t04.stride-ebghtl.rdb # ============================================ # TARGET T0357 # 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 T0357.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 3.34133 # # ============================================ # Comments from T0357.t04.str2.rdb # ============================================ # TARGET T0357 # 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 T0357.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 3.34133 # # ============================================ # Comments from T0357.t04.alpha.rdb # ============================================ # TARGET T0357 # 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 T0357.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 3.34133 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0976 0.0231 0.8793 2 K 0.3130 0.0669 0.6201 3 A 0.7624 0.0318 0.2058 4 I 0.8691 0.0196 0.1113 5 I 0.8495 0.0242 0.1264 6 N 0.6495 0.0263 0.3241 7 K 0.1977 0.1539 0.6484 8 K 0.0829 0.1360 0.7810 9 T 0.1189 0.1356 0.7455 10 E 0.1460 0.1620 0.6919 11 T 0.2837 0.2162 0.5001 12 I 0.4866 0.3438 0.1696 13 I 0.5444 0.3372 0.1184 14 A 0.5628 0.3218 0.1153 15 V 0.4694 0.3744 0.1562 16 G 0.3702 0.3399 0.2899 17 A 0.3622 0.3609 0.2769 18 A 0.3915 0.3452 0.2633 19 M 0.3581 0.3201 0.3218 20 A 0.2224 0.2600 0.5176 21 E 0.1615 0.1931 0.6454 22 I 0.1710 0.0324 0.7966 23 P 0.1855 0.0423 0.7722 24 L 0.3307 0.2866 0.3827 25 V 0.3614 0.3354 0.3032 26 E 0.3900 0.3233 0.2867 27 V 0.2829 0.3415 0.3757 28 R 0.1654 0.2596 0.5750 29 D 0.0930 0.2034 0.7036 30 E 0.0344 0.6482 0.3175 31 K 0.0620 0.6463 0.2917 32 F 0.0561 0.7555 0.1884 33 F 0.0876 0.7684 0.1440 34 E 0.1406 0.7358 0.1237 35 A 0.1295 0.7346 0.1358 36 V 0.1810 0.5776 0.2414 37 K 0.1450 0.4036 0.4514 38 T 0.0473 0.1790 0.7737 39 G 0.0423 0.0328 0.9249 40 D 0.1436 0.0224 0.8341 41 R 0.7822 0.0055 0.2123 42 V 0.8960 0.0039 0.1001 43 V 0.9220 0.0034 0.0746 44 V 0.8930 0.0058 0.1011 45 N 0.6890 0.0058 0.3052 46 A 0.1357 0.0885 0.7758 47 D 0.0847 0.0980 0.8173 48 E 0.0899 0.0655 0.8447 49 G 0.2391 0.0332 0.7276 50 Y 0.7758 0.0147 0.2095 51 V 0.8856 0.0061 0.1083 52 E 0.8981 0.0067 0.0952 53 L 0.8688 0.0110 0.1202 54 I 0.5673 0.0272 0.4055 55 E 0.2827 0.0332 0.6841