# This file is the result of combining several RDB files, specifically # T0469.t06.str2.rdb (weight 1.54425) # T0469.t06.str4.rdb (weight 0.924988) # T0469.t06.pb.rdb (weight 0.789901) # T0469.t06.bys.rdb (weight 0.748322) # T0469.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 T0469.t06.str2.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ # Comments from T0469.t06.str4.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ # Comments from T0469.t06.pb.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ # Comments from T0469.t06.bys.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ # Comments from T0469.t06.alpha.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2440 0.1337 0.6223 2 T 0.2554 0.1237 0.6208 3 Q 0.3111 0.1384 0.5504 4 K 0.3697 0.1359 0.4944 5 F 0.3409 0.1054 0.5537 6 T 0.2059 0.0904 0.7037 7 K 0.0696 0.4065 0.5239 8 D 0.1018 0.2828 0.6153 9 M 0.2515 0.1790 0.5696 10 T 0.2179 0.2270 0.5551 11 F 0.0473 0.7462 0.2065 12 A 0.0150 0.8594 0.1256 13 Q 0.0136 0.9079 0.0786 14 A 0.0192 0.8886 0.0922 15 L 0.0179 0.8400 0.1421 16 Q 0.0230 0.6839 0.2931 17 T 0.0649 0.5388 0.3962 18 H 0.1501 0.1253 0.7246 19 P 0.0321 0.5220 0.4459 20 G 0.0265 0.5234 0.4501 21 V 0.0472 0.6941 0.2587 22 A 0.0362 0.8196 0.1442 23 G 0.0302 0.8653 0.1045 24 V 0.0270 0.8755 0.0975 25 L 0.0324 0.8614 0.1061 26 R 0.0413 0.8115 0.1472 27 S 0.0640 0.6364 0.2996 28 Y 0.0761 0.3652 0.5587 29 N 0.0778 0.1798 0.7425 30 L 0.1561 0.1585 0.6855 31 G 0.1612 0.1861 0.6527 32 C 0.2363 0.1963 0.5674 33 I 0.1949 0.2295 0.5755 34 G 0.1837 0.1559 0.6604 35 C 0.2133 0.1544 0.6323 36 M 0.1465 0.3428 0.5107 37 G 0.1363 0.3911 0.4726 38 A 0.1426 0.3729 0.4845 39 Q 0.0890 0.4544 0.4566 40 N 0.0779 0.5115 0.4106 41 E 0.1160 0.4919 0.3921 42 S 0.1118 0.4880 0.4002 43 L 0.0147 0.8035 0.1819 44 E 0.0089 0.8813 0.1098 45 Q 0.0086 0.9100 0.0814 46 G 0.0092 0.9075 0.0833 47 A 0.0109 0.8850 0.1041 48 N 0.0165 0.8050 0.1784 49 A 0.0251 0.6878 0.2871 50 H 0.0647 0.2371 0.6982 51 G 0.0575 0.1066 0.8359 52 L 0.1879 0.0487 0.7635 53 N 0.1701 0.0276 0.8023 54 V 0.0147 0.7404 0.2448 55 E 0.0101 0.8600 0.1299 56 D 0.0087 0.9177 0.0736 57 I 0.0093 0.9166 0.0741 58 L 0.0086 0.9138 0.0777 59 R 0.0085 0.9139 0.0776 60 D 0.0094 0.8971 0.0935 61 L 0.0187 0.8229 0.1584 62 N 0.0160 0.6494 0.3347 63 A 0.0245 0.4939 0.4816 64 L 0.0918 0.2743 0.6339 65 A 0.0947 0.2263 0.6790