# This file is the result of combining several RDB files, specifically # TR469.t06.str2.rdb (weight 1.54425) # TR469.t06.str4.rdb (weight 0.924988) # TR469.t06.pb.rdb (weight 0.789901) # TR469.t06.bys.rdb (weight 0.748322) # TR469.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 TR469.t06.str2.rdb # ============================================ # TARGET TR469 # 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 TR469.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 20.0325 # # ============================================ # Comments from TR469.t06.str4.rdb # ============================================ # TARGET TR469 # 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 TR469.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 20.0325 # # ============================================ # Comments from TR469.t06.pb.rdb # ============================================ # TARGET TR469 # 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 TR469.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 20.0325 # # ============================================ # Comments from TR469.t06.bys.rdb # ============================================ # TARGET TR469 # 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 TR469.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 20.0325 # # ============================================ # Comments from TR469.t06.alpha.rdb # ============================================ # TARGET TR469 # 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 TR469.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 20.0325 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Q 0.2377 0.1119 0.6504 2 K 0.3016 0.0868 0.6116 3 F 0.2976 0.0777 0.6247 4 T 0.1999 0.0728 0.7273 5 K 0.0642 0.4276 0.5082 6 D 0.1005 0.2939 0.6056 7 M 0.2539 0.1853 0.5608 8 T 0.2192 0.2287 0.5521 9 F 0.0471 0.7502 0.2027 10 A 0.0161 0.8577 0.1262 11 Q 0.0147 0.9063 0.0790 12 A 0.0202 0.8861 0.0937 13 L 0.0183 0.8379 0.1438 14 Q 0.0237 0.6801 0.2962 15 T 0.0657 0.5366 0.3976 16 H 0.1505 0.1245 0.7249 17 P 0.0325 0.5222 0.4453 18 G 0.0269 0.5230 0.4501 19 V 0.0472 0.6926 0.2603 20 A 0.0366 0.8169 0.1465 21 G 0.0308 0.8626 0.1066 22 V 0.0284 0.8722 0.0994 23 L 0.0333 0.8584 0.1083 24 R 0.0427 0.8073 0.1500 25 S 0.0656 0.6318 0.3026 26 Y 0.0767 0.3667 0.5566 27 N 0.0784 0.1834 0.7381 28 L 0.1557 0.1609 0.6834 29 G 0.1603 0.1866 0.6531 30 C 0.2337 0.1960 0.5703 31 I 0.1971 0.2306 0.5724 32 G 0.1896 0.1604 0.6500 33 C 0.2141 0.1630 0.6229 34 M 0.1443 0.3538 0.5019 35 G 0.1315 0.4036 0.4649 36 A 0.1382 0.3862 0.4757 37 Q 0.0868 0.4630 0.4503 38 N 0.0760 0.5211 0.4029 39 E 0.1125 0.5034 0.3842 40 S 0.1079 0.5031 0.3890 41 L 0.0149 0.8070 0.1781 42 E 0.0089 0.8824 0.1087 43 Q 0.0086 0.9097 0.0817 44 G 0.0092 0.9066 0.0842 45 A 0.0110 0.8841 0.1048 46 N 0.0168 0.8029 0.1802 47 A 0.0254 0.6862 0.2884 48 H 0.0651 0.2377 0.6973 49 G 0.0575 0.1072 0.8353 50 L 0.1877 0.0501 0.7622 51 N 0.1700 0.0287 0.8013 52 V 0.0147 0.7401 0.2452 53 E 0.0098 0.8603 0.1298 54 D 0.0087 0.9176 0.0737 55 I 0.0093 0.9166 0.0741 56 L 0.0086 0.9137 0.0778 57 R 0.0085 0.9135 0.0779 58 D 0.0094 0.8960 0.0946 59 L 0.0195 0.8198 0.1608 60 N 0.0163 0.6486 0.3350 61 A 0.0253 0.4939 0.4808 62 L 0.0930 0.2728 0.6342 63 A 0.0953 0.2245 0.6801