# This file is the result of combining several RDB files, specifically # T0366.t04.dssp-ebghstl.rdb (weight 1.53986) # T0366.t04.stride-ebghtl.rdb (weight 1.24869) # T0366.t04.str2.rdb (weight 1.54758) # T0366.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 T0366.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0366 # 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 T0366.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 1856 # # ============================================ # Comments from T0366.t04.stride-ebghtl.rdb # ============================================ # TARGET T0366 # 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 T0366.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 1856 # # ============================================ # Comments from T0366.t04.str2.rdb # ============================================ # TARGET T0366 # 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 T0366.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 1856 # # ============================================ # Comments from T0366.t04.alpha.rdb # ============================================ # TARGET T0366 # 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 T0366.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 1856 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.0632 0.0316 0.9052 2 E 0.0623 0.1570 0.7807 3 N 0.0907 0.1821 0.7272 4 L 0.1060 0.2270 0.6671 5 Y 0.1758 0.1715 0.6527 6 F 0.2071 0.1557 0.6372 7 Q 0.1909 0.1642 0.6449 8 S 0.2088 0.1230 0.6683 9 M 0.1688 0.0764 0.7548 10 G 0.2573 0.0310 0.7118 11 L 0.5653 0.0063 0.4285 12 R 0.7927 0.0114 0.1959 13 T 0.9191 0.0032 0.0777 14 V 0.9218 0.0034 0.0748 15 E 0.9261 0.0032 0.0706 16 M 0.8996 0.0039 0.0965 17 K 0.7821 0.0053 0.2126 18 K 0.5736 0.0225 0.4039 19 G 0.1533 0.0173 0.8294 20 P 0.0654 0.0692 0.8654 21 T 0.0557 0.0779 0.8664 22 D 0.0973 0.0833 0.8194 23 S 0.2074 0.0590 0.7336 24 L 0.4873 0.0284 0.4843 25 G 0.6968 0.0111 0.2921 26 I 0.8657 0.0050 0.1293 27 S 0.9075 0.0039 0.0885 28 I 0.8944 0.0058 0.0998 29 A 0.7747 0.0210 0.2043 30 G 0.4819 0.0248 0.4933 31 G 0.2719 0.0313 0.6968 32 V 0.2979 0.0504 0.6517 33 G 0.2151 0.0416 0.7433 34 S 0.1115 0.0379 0.8505 35 P 0.0795 0.0949 0.8256 36 L 0.0696 0.0975 0.8329 37 G 0.0684 0.0711 0.8606 38 D 0.1178 0.0467 0.8355 39 V 0.2727 0.0185 0.7089 40 P 0.6205 0.0129 0.3666 41 I 0.8570 0.0069 0.1361 42 F 0.9131 0.0043 0.0826 43 I 0.9047 0.0049 0.0904 44 A 0.8399 0.0323 0.1278 45 M 0.7713 0.0099 0.2188 46 M 0.7236 0.0114 0.2650 47 H 0.3633 0.0227 0.6140 48 P 0.1006 0.0856 0.8138 49 T 0.0491 0.0704 0.8805 50 G 0.0961 0.1712 0.7327 51 V 0.0591 0.6377 0.3032 52 A 0.0767 0.6415 0.2818 53 A 0.0954 0.6203 0.2843 54 Q 0.1023 0.4903 0.4073 55 T 0.1011 0.2017 0.6972 56 Q 0.1054 0.1119 0.7827 57 K 0.2733 0.0585 0.6683 58 L 0.4070 0.0248 0.5682 59 R 0.1496 0.0255 0.8249 60 V 0.0519 0.1055 0.8426 61 G 0.0542 0.0465 0.8993 62 D 0.3178 0.0238 0.6585 63 R 0.8118 0.0079 0.1804 64 I 0.9135 0.0042 0.0823 65 V 0.9154 0.0057 0.0790 66 T 0.9128 0.0037 0.0835 67 I 0.8468 0.0175 0.1357 68 C 0.4445 0.0194 0.5361 69 G 0.2083 0.0282 0.7635 70 T 0.4935 0.0171 0.4894 71 S 0.5570 0.0219 0.4211 72 T 0.2121 0.1089 0.6790 73 E 0.0715 0.0972 0.8313 74 G 0.0474 0.0659 0.8866 75 M 0.1339 0.0258 0.8403 76 T 0.1355 0.0317 0.8328 77 H 0.0047 0.9464 0.0489 78 T 0.0047 0.9603 0.0351 79 Q 0.0047 0.9610 0.0344 80 A 0.0047 0.9610 0.0343 81 V 0.0047 0.9612 0.0342 82 N 0.0046 0.9607 0.0347 83 L 0.0047 0.9576 0.0377 84 L 0.0049 0.9459 0.0491 85 K 0.0057 0.8952 0.0991 86 N 0.0098 0.6430 0.3472 87 A 0.0611 0.2089 0.7300 88 S 0.0350 0.0710 0.8940 89 G 0.0642 0.0299 0.9059 90 S 0.5029 0.0125 0.4845 91 I 0.8716 0.0037 0.1247 92 E 0.9142 0.0033 0.0824 93 M 0.9263 0.0032 0.0705 94 Q 0.9224 0.0037 0.0739 95 V 0.9144 0.0035 0.0821 96 V 0.7576 0.0086 0.2338 97 A 0.4813 0.0209 0.4978 98 G 0.1248 0.0380 0.8372 99 G 0.0896 0.0312 0.8792 100 D 0.1621 0.0388 0.7991 101 V 0.2034 0.0649 0.7317 102 S 0.1461 0.0587 0.7952 103 E 0.1373 0.0569 0.8058 104 T 0.1014 0.0502 0.8485 105 S 0.0890 0.0346 0.8764 106 V 0.0536 0.0460 0.9005