# This file is the result of combining several RDB files, specifically # T0409.t06.str2.rdb (weight 1.54425) # T0409.t06.str4.rdb (weight 0.924988) # T0409.t06.pb.rdb (weight 0.789901) # T0409.t06.bys.rdb (weight 0.748322) # T0409.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 T0409.t06.str2.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ # Comments from T0409.t06.str4.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ # Comments from T0409.t06.pb.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ # Comments from T0409.t06.bys.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ # Comments from T0409.t06.alpha.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.2158 0.1083 0.6760 2 R 0.1913 0.0912 0.7175 3 G 0.1664 0.0668 0.7668 4 P 0.0925 0.4713 0.4363 5 E 0.0528 0.6556 0.2916 6 A 0.0808 0.6519 0.2673 7 F 0.1601 0.4993 0.3406 8 L 0.2289 0.3179 0.4531 9 K 0.2120 0.1889 0.5991 10 L 0.2297 0.0604 0.7099 11 P 0.1505 0.1118 0.7377 12 K 0.0583 0.3616 0.5801 13 D 0.0899 0.3159 0.5942 14 L 0.0612 0.5179 0.4209 15 K 0.0611 0.5261 0.4128 16 D 0.0805 0.5325 0.3870 17 R 0.0122 0.8245 0.1633 18 E 0.0092 0.8833 0.1076 19 A 0.0090 0.9140 0.0770 20 L 0.0091 0.9154 0.0755 21 Q 0.0085 0.9144 0.0771 22 D 0.0085 0.9136 0.0779 23 I 0.0091 0.9029 0.0880 24 M 0.0122 0.8733 0.1144 25 Q 0.0121 0.7396 0.2483 26 D 0.0223 0.4994 0.4783 27 I 0.1102 0.1897 0.7001 28 G 0.0795 0.2545 0.6660 29 N 0.1045 0.1876 0.7079 30 S 0.0964 0.3114 0.5922 31 D 0.0692 0.4062 0.5247 32 D 0.1287 0.3097 0.5616 33 I 0.2853 0.1669 0.5479 34 L 0.3805 0.1287 0.4908 35 A 0.4821 0.1843 0.3337 36 A 0.6774 0.0934 0.2292 37 V 0.7514 0.0574 0.1912 38 V 0.7084 0.0393 0.2523 39 L 0.6612 0.0514 0.2874 40 S 0.6063 0.0366 0.3572 41 A 0.5223 0.0289 0.4488 42 T 0.3571 0.0164 0.6265 43 P 0.1270 0.2464 0.6266 44 G 0.1036 0.1883 0.7081 45 A 0.5016 0.0695 0.4289 46 V 0.7392 0.0137 0.2472 47 E 0.7842 0.0214 0.1944 48 A 0.8176 0.0069 0.1754 49 F 0.7894 0.0179 0.1927 50 R 0.6929 0.0224 0.2848 51 K 0.5251 0.1319 0.3430 52 N 0.1542 0.1061 0.7397 53 G 0.1018 0.0571 0.8410 54 E 0.4123 0.0237 0.5640 55 T 0.6951 0.0088 0.2962 56 I 0.7591 0.0101 0.2308 57 R 0.7820 0.0062 0.2118 58 I 0.7263 0.0108 0.2629 59 T 0.4727 0.0333 0.4940 60 G 0.2177 0.1644 0.6179 61 D 0.1018 0.3451 0.5531 62 G 0.0902 0.4409 0.4689 63 L 0.0685 0.6920 0.2396 64 K 0.0289 0.8367 0.1344 65 A 0.0243 0.8474 0.1284 66 A 0.0259 0.8461 0.1280 67 H 0.0224 0.8541 0.1235 68 R 0.0215 0.8162 0.1622 69 F 0.0354 0.6949 0.2697 70 L 0.0708 0.5118 0.4174 71 S 0.0834 0.4043 0.5123 72 N 0.0780 0.2862 0.6358 73 D 0.1573 0.1144 0.7283 74 P 0.0977 0.3150 0.5874 75 K 0.0986 0.3283 0.5731 76 I 0.1323 0.3329 0.5349 77 G 0.0761 0.5206 0.4032 78 E 0.0728 0.5702 0.3571 79 K 0.1468 0.4284 0.4248 80 R 0.2762 0.2347 0.4891 81 I 0.3624 0.0791 0.5585 82 R 0.2482 0.0361 0.7157 83 P 0.1326 0.1536 0.7138 84 G 0.0924 0.0937 0.8139 85 A 0.4572 0.0252 0.5176 86 L 0.7179 0.0095 0.2727 87 I 0.7968 0.0070 0.1961 88 R 0.7836 0.0075 0.2089 89 V 0.7700 0.0094 0.2207 90 K 0.7624 0.0171 0.2205 91 K 0.6795 0.0348 0.2857 92 T 0.5085 0.0622 0.4293 93 E 0.2263 0.2199 0.5538 94 K 0.1292 0.1331 0.7377 95 G 0.1086 0.0788 0.8125 96 S 0.4213 0.0293 0.5494 97 W 0.6951 0.0113 0.2936 98 Q 0.7643 0.0121 0.2236 99 I 0.7664 0.0216 0.2120 100 V 0.7393 0.0324 0.2283 101 Q 0.7005 0.0236 0.2759 102 L 0.5163 0.0160 0.4677 103 P 0.2762 0.0322 0.6916