# This file is the result of combining several RDB files, specifically # T0348.t04.dssp-ebghstl.rdb (weight 1.53986) # T0348.t04.stride-ebghtl.rdb (weight 1.24869) # T0348.t04.str2.rdb (weight 1.54758) # T0348.t04.alpha.rdb (weight 0.659012) # 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 T0348.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0348 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0348.t04-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 28.2264 # # ============================================ # Comments from T0348.t04.stride-ebghtl.rdb # ============================================ # TARGET T0348 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0348.t04-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 28.2264 # # ============================================ # Comments from T0348.t04.str2.rdb # ============================================ # TARGET T0348 # Using neural net t04-2621-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 T0348.t04-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 28.2264 # # ============================================ # Comments from T0348.t04.alpha.rdb # ============================================ # TARGET T0348 # Using neural net t04-2621-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 T0348.t04-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 28.2264 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0586 0.0381 0.9033 2 D 0.0710 0.0434 0.8855 3 A 0.0069 0.8200 0.1731 4 K 0.0073 0.8574 0.1353 5 F 0.0084 0.8894 0.1022 6 L 0.0163 0.8681 0.1156 7 E 0.0264 0.8586 0.1149 8 I 0.0465 0.8257 0.1278 9 L 0.0931 0.7055 0.2014 10 V 0.1672 0.4141 0.4188 11 C 0.1496 0.1121 0.7384 12 P 0.0702 0.2260 0.7038 13 L 0.0763 0.1948 0.7289 14 C 0.1453 0.1084 0.7463 15 K 0.1015 0.0776 0.8209 16 G 0.1462 0.0432 0.8107 17 P 0.3215 0.0679 0.6105 18 L 0.5124 0.0525 0.4351 19 V 0.7557 0.0314 0.2129 20 F 0.7711 0.0272 0.2016 21 D 0.5582 0.0262 0.4156 22 K 0.2173 0.1969 0.5857 23 S 0.1976 0.1733 0.6291 24 K 0.1054 0.1224 0.7722 25 D 0.1141 0.0798 0.8061 26 E 0.6509 0.0535 0.2956 27 L 0.7956 0.0283 0.1760 28 I 0.7632 0.0298 0.2071 29 C 0.5235 0.0285 0.4480 30 K 0.1165 0.1799 0.7036 31 G 0.0877 0.1584 0.7539 32 D 0.1609 0.2064 0.6327 33 R 0.1821 0.2343 0.5836 34 L 0.3641 0.1379 0.4980 35 A 0.5497 0.0901 0.3603 36 F 0.5043 0.0387 0.4570 37 P 0.4775 0.0356 0.4869 38 I 0.3375 0.1506 0.5119 39 K 0.2357 0.1779 0.5864 40 D 0.0750 0.1384 0.7866 41 G 0.0892 0.0701 0.8407 42 I 0.2558 0.0336 0.7106 43 P 0.5574 0.0467 0.3958 44 M 0.6101 0.0944 0.2954 45 M 0.5372 0.0880 0.3748 46 L 0.3283 0.0891 0.5826 47 E 0.1011 0.5186 0.3804 48 S 0.0442 0.6887 0.2671 49 E 0.0304 0.7328 0.2368 50 A 0.0534 0.6665 0.2801 51 R 0.0714 0.5659 0.3627 52 E 0.0872 0.3996 0.5132 53 L 0.0854 0.1307 0.7839 54 A 0.0567 0.0199 0.9234 55 P 0.0108 0.6121 0.3771 56 E 0.0106 0.7058 0.2836 57 E 0.0239 0.7441 0.2320 58 E 0.0602 0.6978 0.2420 59 V 0.1217 0.6018 0.2764 60 K 0.1319 0.5301 0.3380 61 L 0.1018 0.5326 0.3655 62 E 0.0884 0.4771 0.4345 63 H 0.0765 0.4837 0.4398 64 H 0.0751 0.3736 0.5513 65 H 0.0912 0.2673 0.6415 66 H 0.0818 0.1762 0.7420 67 H 0.0639 0.0827 0.8534 68 H 0.0499 0.0373 0.9128