# This file is the result of combining several RDB files, specifically # T0475.t04.dssp-ebghstl.rdb (weight 1.53986) # T0475.t04.stride-ebghtl.rdb (weight 1.24869) # T0475.t04.str2.rdb (weight 1.54758) # T0475.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 T0475.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0475 # Using neural net t04-2621-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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.stride-ebghtl.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.str2.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ # Comments from T0475.t04.alpha.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1280 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0578 0.0278 0.9144 2 N 0.0604 0.0457 0.8939 3 S 0.0168 0.5453 0.4379 4 E 0.0166 0.6713 0.3121 5 I 0.0170 0.7332 0.2498 6 E 0.0097 0.7875 0.2028 7 L 0.0050 0.9472 0.0478 8 P 0.0052 0.9529 0.0419 9 V 0.0047 0.9582 0.0371 10 Q 0.0047 0.9593 0.0360 11 K 0.0047 0.9571 0.0382 12 Q 0.0047 0.9570 0.0383 13 L 0.0047 0.9584 0.0369 14 E 0.0047 0.9569 0.0384 15 A 0.0049 0.9529 0.0422 16 Y 0.0055 0.9142 0.0803 17 N 0.0079 0.7273 0.2648 18 A 0.0187 0.5137 0.4676 19 R 0.0304 0.2979 0.6717 20 D 0.0872 0.1276 0.7852 21 I 0.0051 0.9349 0.0600 22 D 0.0048 0.9559 0.0393 23 A 0.0047 0.9579 0.0374 24 F 0.0053 0.9542 0.0405 25 M 0.0058 0.9415 0.0527 26 A 0.0073 0.8891 0.1036 27 W 0.0143 0.7472 0.2384 28 W 0.0397 0.5046 0.4557 29 A 0.0520 0.2146 0.7334 30 D 0.0205 0.2192 0.7603 31 D 0.0576 0.1094 0.8330 32 C 0.4290 0.0627 0.5083 33 Q 0.8168 0.0364 0.1468 34 Y 0.8729 0.0198 0.1072 35 Y 0.7722 0.0261 0.2017 36 A 0.4429 0.0243 0.5328 37 F 0.1506 0.0295 0.8198 38 P 0.0856 0.1146 0.7998 39 A 0.0699 0.1811 0.7490 40 T 0.0972 0.2390 0.6638 41 L 0.1799 0.2439 0.5763 42 L 0.2498 0.2467 0.5035 43 A 0.1986 0.2519 0.5495 44 G 0.1109 0.1844 0.7048 45 N 0.0673 0.1696 0.7631 46 A 0.0071 0.9200 0.0729 47 A 0.0049 0.9565 0.0386 48 E 0.0047 0.9598 0.0355 49 I 0.0047 0.9596 0.0357 50 R 0.0047 0.9590 0.0363 51 V 0.0047 0.9562 0.0391 52 R 0.0048 0.9506 0.0446 53 H 0.0056 0.9391 0.0553 54 I 0.0057 0.9313 0.0630 55 E 0.0073 0.8876 0.1051 56 R 0.0141 0.7711 0.2149 57 F 0.0490 0.3671 0.5839 58 K 0.0446 0.1355 0.8199 59 E 0.0706 0.0352 0.8942 60 P 0.0496 0.1189 0.8315 61 D 0.0841 0.1120 0.8039 62 L 0.2626 0.0979 0.6395 63 Y 0.5046 0.0524 0.4430 64 G 0.6993 0.0224 0.2783 65 E 0.8077 0.0127 0.1795 66 L 0.8537 0.0106 0.1357 67 L 0.8004 0.0275 0.1722 68 T 0.8567 0.0135 0.1298 69 R 0.8867 0.0122 0.1012 70 V 0.8901 0.0113 0.0986 71 I 0.8232 0.0196 0.1572 72 V 0.5331 0.0288 0.4380 73 G 0.1606 0.0400 0.7994 74 N 0.2748 0.0406 0.6846 75 V 0.8178 0.0095 0.1727 76 V 0.9060 0.0048 0.0893 77 I 0.9137 0.0045 0.0818 78 D 0.9007 0.0066 0.0926 79 H 0.8696 0.0125 0.1179 80 E 0.8644 0.0087 0.1269 81 T 0.8814 0.0099 0.1087 82 V 0.8705 0.0126 0.1168 83 T 0.8309 0.0190 0.1502 84 R 0.8117 0.0186 0.1697 85 N 0.6950 0.0194 0.2856 86 F 0.3662 0.0242 0.6095 87 P 0.0782 0.0517 0.8701 88 E 0.0465 0.0507 0.9028 89 G 0.1812 0.0389 0.7799 90 K 0.4573 0.0380 0.5046 91 G 0.6470 0.0179 0.3351 92 E 0.7901 0.0111 0.1988 93 V 0.7667 0.0075 0.2257 94 D 0.7579 0.0129 0.2292 95 V 0.8996 0.0053 0.0951 96 A 0.9083 0.0039 0.0878 97 C 0.9210 0.0034 0.0755 98 I 0.9205 0.0035 0.0760 99 Y 0.9190 0.0041 0.0769 100 E 0.9240 0.0037 0.0723 101 V 0.8244 0.0108 0.1647 102 E 0.3713 0.0249 0.6038 103 N 0.0491 0.0219 0.9289 104 G 0.0687 0.0314 0.8998 105 R 0.7529 0.0149 0.2322 106 I 0.9201 0.0039 0.0760 107 A 0.8865 0.0167 0.0968 108 K 0.9155 0.0064 0.0781 109 A 0.9059 0.0118 0.0823 110 W 0.8885 0.0206 0.0909 111 F 0.8353 0.0391 0.1256 112 K 0.7080 0.0629 0.2291 113 I 0.3979 0.0678 0.5343 114 G 0.1063 0.0505 0.8432 115 E 0.0973 0.1195 0.7832 116 P 0.1019 0.3770 0.5210 117 R 0.1371 0.4633 0.3996 118 I 0.1522 0.5221 0.3257 119 V 0.1919 0.4122 0.3959 120 S 0.1664 0.2715 0.5621 121 Q 0.0961 0.0576 0.8463 122 K 0.0581 0.0357 0.9062