# This file is the result of combining several RDB files, specifically # T0404.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0404.t2k.stride-ebghtl.rdb (weight 1.24869) # T0404.t2k.str.rdb (weight 1.53983) # 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 T0404.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0404 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0404.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 46 # # ============================================ # Comments from T0404.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0404 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0404.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 46 # # ============================================ # Comments from T0404.t2k.str.rdb # ============================================ # TARGET T0404 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0404.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 46 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0186 0.0082 0.9732 2 S 0.1219 0.0189 0.8592 3 K 0.1544 0.0271 0.8185 4 R 0.2319 0.0477 0.7204 5 A 0.3547 0.0572 0.5881 6 N 0.6497 0.0424 0.3079 7 K 0.8588 0.0252 0.1160 8 L 0.9247 0.0285 0.0469 9 V 0.9400 0.0330 0.0271 10 I 0.8962 0.0573 0.0464 11 V 0.8241 0.0565 0.1194 12 T 0.5806 0.1211 0.2983 13 E 0.1635 0.1960 0.6405 14 K 0.0367 0.5536 0.4097 15 V 0.0169 0.7090 0.2741 16 L 0.0100 0.7517 0.2384 17 L 0.0055 0.8515 0.1430 18 K 0.0053 0.8766 0.1181 19 K 0.0044 0.9306 0.0649 20 V 0.0038 0.9685 0.0278 21 A 0.0037 0.9754 0.0209 22 K 0.0037 0.9749 0.0214 23 I 0.0037 0.9759 0.0204 24 I 0.0037 0.9760 0.0203 25 E 0.0037 0.9728 0.0235 26 E 0.0038 0.9429 0.0533 27 A 0.0044 0.4625 0.5331 28 G 0.0092 0.0114 0.9794 29 A 0.0334 0.0072 0.9594 30 T 0.1413 0.0132 0.8455 31 G 0.6192 0.0156 0.3652 32 Y 0.8696 0.0048 0.1256 33 T 0.9394 0.0041 0.0565 34 V 0.8914 0.0061 0.1025 35 V 0.6266 0.0117 0.3617 36 D 0.4125 0.0262 0.5613 37 T 0.2725 0.0473 0.6802 38 G 0.1915 0.0244 0.7841 39 G 0.2030 0.0306 0.7664 40 K 0.2796 0.0314 0.6889 41 G 0.1957 0.0463 0.7580 42 S 0.1334 0.0650 0.8015 43 R 0.0897 0.0607 0.8495 44 N 0.1219 0.0676 0.8105 45 V 0.3387 0.0569 0.6044 46 R 0.4963 0.0604 0.4433 47 S 0.2736 0.0937 0.6327 48 T 0.0935 0.1058 0.8007 49 G 0.0876 0.1007 0.8116 50 K 0.1958 0.1165 0.6877 51 P 0.2235 0.1527 0.6238 52 N 0.2365 0.1689 0.5946 53 T 0.2264 0.1679 0.6057 54 S 0.2855 0.1559 0.5586 55 D 0.4198 0.1344 0.4458 56 T 0.4779 0.1249 0.3972 57 D 0.4845 0.1573 0.3583 58 S 0.4211 0.1556 0.4233 59 N 0.4499 0.1083 0.4418 60 V 0.5696 0.0571 0.3733 61 K 0.7037 0.0125 0.2838 62 F 0.9249 0.0035 0.0716 63 E 0.9647 0.0025 0.0328 64 V 0.9720 0.0024 0.0256 65 L 0.9565 0.0025 0.0410 66 T 0.9111 0.0025 0.0864 67 E 0.6636 0.0028 0.3336 68 N 0.1704 0.0067 0.8229 69 R 0.0134 0.5756 0.4110 70 E 0.0049 0.8508 0.1443 71 M 0.0040 0.8938 0.1022 72 A 0.0043 0.8954 0.1003 73 E 0.0040 0.9035 0.0925 74 K 0.0048 0.8986 0.0966 75 I 0.0040 0.9177 0.0783 76 A 0.0047 0.9323 0.0629 77 D 0.0043 0.9305 0.0652 78 Q 0.0040 0.9256 0.0704 79 V 0.0042 0.9090 0.0868 80 A 0.0046 0.8887 0.1067 81 I 0.0064 0.8578 0.1357 82 K 0.0088 0.7413 0.2499 83 F 0.0210 0.6603 0.3188 84 F 0.0642 0.4451 0.4906 85 T 0.0272 0.3550 0.6178 86 D 0.0207 0.1536 0.8257 87 Y 0.1944 0.0441 0.7615 88 A 0.5384 0.0092 0.4524 89 G 0.9195 0.0034 0.0771 90 I 0.9699 0.0024 0.0277 91 I 0.9746 0.0024 0.0230 92 Y 0.9698 0.0024 0.0278 93 I 0.9093 0.0027 0.0880 94 C 0.7110 0.0084 0.2806 95 E 0.5908 0.0177 0.3916 96 A 0.7005 0.0200 0.2795 97 E 0.8087 0.0155 0.1758 98 V 0.8810 0.0109 0.1081 99 L 0.8132 0.0137 0.1731 100 Y 0.5307 0.0207 0.4486 101 G 0.1572 0.2295 0.6133 102 R 0.1429 0.2656 0.5916 103 T 0.2235 0.3239 0.4526 104 F 0.2304 0.1060 0.6637 105 C 0.1936 0.0598 0.7466 106 G 0.0535 0.0427 0.9037 107 P 0.0276 0.0695 0.9029 108 D 0.0443 0.0702 0.8855 109 G 0.0516 0.0401 0.9083 110 C 0.0107 0.0057 0.9836