# This file is the result of combining several RDB files, specifically # TR476.t06.str2.rdb (weight 1.54425) # TR476.t06.str4.rdb (weight 0.924988) # TR476.t06.pb.rdb (weight 0.789901) # TR476.t06.bys.rdb (weight 0.748322) # TR476.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 TR476.t06.str2.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t06.str4.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t06.pb.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t06.bys.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t06.alpha.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.2636 0.1047 0.6317 2 K 0.2537 0.0809 0.6654 3 C 0.2797 0.0328 0.6874 4 P 0.2314 0.1243 0.6443 5 I 0.2862 0.1858 0.5280 6 C 0.2109 0.1267 0.6624 7 G 0.1313 0.0856 0.7831 8 S 0.2077 0.0645 0.7278 9 P 0.2089 0.1727 0.6184 10 L 0.2361 0.2049 0.5590 11 K 0.1855 0.1611 0.6534 12 W 0.0210 0.7385 0.2405 13 E 0.0092 0.8684 0.1224 14 E 0.0084 0.9192 0.0725 15 L 0.0085 0.9189 0.0726 16 I 0.0084 0.9173 0.0743 17 E 0.0083 0.9192 0.0725 18 E 0.0085 0.9141 0.0773 19 M 0.0106 0.8965 0.0930 20 L 0.0165 0.8571 0.1265 21 I 0.0379 0.7650 0.1970 22 I 0.0441 0.7367 0.2192 23 E 0.0481 0.5886 0.3633 24 N 0.0632 0.4886 0.4482 25 F 0.0285 0.7520 0.2195 26 E 0.0133 0.8566 0.1301 27 E 0.0183 0.8677 0.1140 28 I 0.0324 0.8255 0.1420 29 V 0.0512 0.7868 0.1621 30 K 0.0442 0.7518 0.2040 31 D 0.0675 0.6817 0.2509 32 R 0.0118 0.8461 0.1421 33 E 0.0096 0.8931 0.0973 34 R 0.0101 0.9063 0.0836 35 F 0.0125 0.8969 0.0905 36 L 0.0113 0.8945 0.0942 37 A 0.0104 0.8662 0.1234 38 Q 0.0167 0.8165 0.1668 39 V 0.0421 0.7481 0.2097 40 E 0.0403 0.7217 0.2380 41 E 0.1008 0.5577 0.3415 42 F 0.2523 0.3662 0.3815 43 V 0.4031 0.2370 0.3598 44 F 0.4906 0.1282 0.3812 45 K 0.4061 0.0870 0.5069 46 C 0.2818 0.0375 0.6806 47 P 0.1684 0.1758 0.6559 48 V 0.1896 0.1998 0.6105 49 C 0.1624 0.1698 0.6679 50 G 0.1250 0.2132 0.6618 51 E 0.2065 0.3602 0.4333 52 E 0.2874 0.3963 0.3164 53 F 0.3085 0.3168 0.3747 54 Y 0.2542 0.2165 0.5293 55 G 0.1658 0.1983 0.6359 56 K 0.2467 0.2336 0.5196 57 T 0.2581 0.1702 0.5717 58 L 0.2535 0.0692 0.6773 59 P 0.1725 0.0897 0.7378 60 R 0.0537 0.5806 0.3657 61 R 0.0298 0.7376 0.2326 62 E 0.0288 0.7843 0.1869 63 A 0.0176 0.8654 0.1170 64 E 0.0112 0.8994 0.0894 65 K 0.0114 0.9062 0.0824 66 V 0.0134 0.9057 0.0809 67 F 0.0147 0.9052 0.0801 68 E 0.0202 0.8948 0.0850 69 L 0.0270 0.8629 0.1101 70 L 0.0461 0.7567 0.1972 71 N 0.0609 0.5796 0.3595 72 D 0.0779 0.4328 0.4893 73 F 0.1081 0.2963 0.5956 74 K 0.1253 0.2133 0.6614 75 G 0.1503 0.1245 0.7252 76 G 0.2835 0.0918 0.6247 77 I 0.4389 0.0602 0.5009 78 D 0.3287 0.0448 0.6264 79 W 0.1401 0.3742 0.4858 80 E 0.1012 0.3553 0.5434 81 N 0.1931 0.1810 0.6258 82 K 0.3704 0.0959 0.5337 83 R 0.5499 0.0393 0.4108 84 V 0.6815 0.0176 0.3009 85 K 0.6856 0.0166 0.2978 86 L 0.6239 0.0220 0.3541 87 K 0.4780 0.0492 0.4729