# This file is the result of combining several RDB files, specifically # TR429.t06.str2.rdb (weight 1.54425) # TR429.t06.str4.rdb (weight 0.924988) # TR429.t06.pb.rdb (weight 0.789901) # TR429.t06.bys.rdb (weight 0.748322) # TR429.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 TR429.t06.str2.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.71788 # # ============================================ # Comments from TR429.t06.str4.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.71788 # # ============================================ # Comments from TR429.t06.pb.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.71788 # # ============================================ # Comments from TR429.t06.bys.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.71788 # # ============================================ # Comments from TR429.t06.alpha.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.71788 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.2328 0.1851 0.5820 2 A 0.2578 0.2643 0.4779 3 R 0.2941 0.3236 0.3824 4 T 0.4429 0.2658 0.2914 5 I 0.5068 0.1804 0.3128 6 I 0.5582 0.1125 0.3293 7 K 0.3977 0.1032 0.4990 8 W 0.1975 0.3185 0.4840 9 Q 0.1351 0.3925 0.4724 10 D 0.1672 0.3237 0.5091 11 L 0.3005 0.1571 0.5423 12 E 0.3003 0.1115 0.5881 13 V 0.2252 0.1459 0.6289 14 G 0.1915 0.0900 0.7186 15 Q 0.4921 0.0320 0.4760 16 V 0.7393 0.0096 0.2510 17 V 0.7903 0.0096 0.2001 18 M 0.8014 0.0071 0.1915 19 L 0.7653 0.0151 0.2196 20 N 0.6240 0.0273 0.3487 21 Y 0.4548 0.0434 0.5017 22 N 0.2615 0.0240 0.7145 23 P 0.0538 0.3845 0.5617 24 D 0.0555 0.3105 0.6340 25 N 0.1366 0.1958 0.6676 26 P 0.0960 0.3752 0.5288 27 K 0.0886 0.4076 0.5039 28 E 0.1234 0.3379 0.5387 29 R 0.1919 0.1602 0.6479 30 G 0.2833 0.0879 0.6288 31 F 0.5689 0.0479 0.3832 32 W 0.6945 0.0473 0.2581 33 Y 0.6593 0.0759 0.2649 34 D 0.5962 0.0974 0.3064 35 A 0.5647 0.2079 0.2274 36 E 0.5897 0.1924 0.2180 37 I 0.5638 0.2046 0.2316 38 S 0.4087 0.2905 0.3008 39 R 0.3555 0.2758 0.3686 40 K 0.2971 0.2754 0.4276 41 R 0.2420 0.2916 0.4663 42 E 0.1931 0.2927 0.5142 43 T 0.1973 0.2667 0.5360 44 R 0.1901 0.2811 0.5289 45 T 0.2399 0.2512 0.5089 46 A 0.1716 0.4493 0.3791 47 R 0.2092 0.4546 0.3362 48 E 0.4279 0.2783 0.2939 49 L 0.5692 0.1411 0.2898 50 Y 0.6668 0.0834 0.2498 51 A 0.7463 0.0430 0.2108 52 N 0.7388 0.0374 0.2238 53 V 0.7688 0.0229 0.2083 54 V 0.7024 0.0371 0.2604 55 L 0.5605 0.0488 0.3907 56 G 0.2503 0.0547 0.6950 57 D 0.1560 0.1855 0.6585 58 D 0.1313 0.2265 0.6422 59 S 0.1747 0.2495 0.5758 60 L 0.1821 0.2483 0.5696 61 N 0.1452 0.2399 0.6149 62 D 0.1732 0.1856 0.6413 63 C 0.3618 0.0935 0.5447 64 R 0.5535 0.0631 0.3834 65 I 0.7086 0.0357 0.2557 66 I 0.6932 0.0453 0.2615 67 F 0.6324 0.0613 0.3063 68 V 0.4229 0.2416 0.3355 69 D 0.3365 0.3542 0.3093 70 E 0.3885 0.3373 0.2742 71 V 0.5204 0.2120 0.2675 72 F 0.5801 0.1349 0.2850 73 K 0.6382 0.0872 0.2746 74 I 0.5950 0.0664 0.3386 75 E 0.5189 0.0641 0.4170 76 R 0.3690 0.0346 0.5964 77 P 0.2195 0.0911 0.6894