# This file is the result of combining several RDB files, specifically # T0387.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0387.t2k.stride-ebghtl.rdb (weight 1.24869) # T0387.t2k.str2.rdb (weight 1.54758) # T0387.t2k.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 T0387.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0387 # 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 T0387.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 2308 # # ============================================ # Comments from T0387.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0387 # 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 T0387.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 2308 # # ============================================ # Comments from T0387.t2k.str2.rdb # ============================================ # TARGET T0387 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0387.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 2308 # # ============================================ # Comments from T0387.t2k.alpha.rdb # ============================================ # TARGET T0387 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0387.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 2308 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1047 0.0323 0.8631 2 M 0.2135 0.0145 0.7720 3 K 0.3967 0.0130 0.5903 4 P 0.6113 0.0121 0.3765 5 K 0.8122 0.0113 0.1765 6 L 0.8979 0.0031 0.0990 7 C 0.8917 0.0041 0.1041 8 R 0.9035 0.0038 0.0927 9 L 0.8606 0.0055 0.1338 10 A 0.7333 0.0133 0.2534 11 K 0.4760 0.0249 0.4990 12 G 0.1133 0.0494 0.8373 13 E 0.0800 0.0702 0.8498 14 N 0.1571 0.0453 0.7976 15 G 0.3916 0.0397 0.5687 16 Y 0.6327 0.0193 0.3480 17 G 0.8102 0.0121 0.1778 18 F 0.8756 0.0069 0.1175 19 H 0.8905 0.0062 0.1033 20 L 0.8923 0.0078 0.0999 21 N 0.8408 0.0169 0.1423 22 A 0.6866 0.0293 0.2841 23 I 0.4078 0.0523 0.5399 24 R 0.2163 0.0791 0.7046 25 G 0.1486 0.0752 0.7762 26 L 0.1593 0.0527 0.7880 27 P 0.2005 0.0498 0.7497 28 G 0.5212 0.0244 0.4544 29 S 0.8406 0.0053 0.1541 30 F 0.9027 0.0044 0.0929 31 I 0.9033 0.0038 0.0928 32 K 0.8291 0.0266 0.1442 33 E 0.8001 0.0087 0.1912 34 V 0.6719 0.0143 0.3137 35 Q 0.2518 0.0199 0.7284 36 K 0.0428 0.0701 0.8870 37 G 0.0279 0.0441 0.9281 38 G 0.0648 0.1023 0.8329 39 P 0.0380 0.7549 0.2070 40 A 0.0124 0.8578 0.1299 41 D 0.0100 0.8629 0.1271 42 L 0.0200 0.8149 0.1651 43 A 0.0437 0.3741 0.5822 44 G 0.0322 0.0540 0.9138 45 L 0.1085 0.0132 0.8783 46 E 0.1108 0.0198 0.8694 47 D 0.0382 0.1964 0.7655 48 E 0.0574 0.1102 0.8323 49 D 0.3681 0.0596 0.5723 50 V 0.8287 0.0112 0.1602 51 I 0.8979 0.0068 0.0953 52 I 0.9098 0.0059 0.0843 53 E 0.8947 0.0092 0.0961 54 V 0.8064 0.0179 0.1757 55 N 0.1284 0.0265 0.8451 56 G 0.0496 0.0504 0.9000 57 V 0.5692 0.0207 0.4101 58 N 0.5970 0.0191 0.3840 59 V 0.4392 0.0688 0.4920 60 L 0.2271 0.0963 0.6767 61 D 0.0958 0.0784 0.8258 62 E 0.1446 0.0407 0.8147 63 P 0.1363 0.0491 0.8145 64 Y 0.0057 0.9092 0.0851 65 E 0.0048 0.9508 0.0445 66 K 0.0049 0.9562 0.0389 67 V 0.0047 0.9581 0.0372 68 V 0.0047 0.9579 0.0374 69 D 0.0048 0.9553 0.0400 70 R 0.0050 0.9482 0.0468 71 I 0.0086 0.9273 0.0641 72 Q 0.0120 0.8466 0.1414 73 S 0.0322 0.4994 0.4684 74 S 0.0605 0.1286 0.8109 75 G 0.0416 0.0753 0.8831 76 K 0.0506 0.0569 0.8925 77 N 0.3334 0.0156 0.6510 78 V 0.7990 0.0042 0.1968 79 T 0.9060 0.0037 0.0903 80 L 0.9233 0.0033 0.0734 81 L 0.9205 0.0034 0.0761 82 V 0.9075 0.0034 0.0891 83 C 0.8273 0.0056 0.1670 84 G 0.5498 0.0111 0.4391 85 K 0.1825 0.0313 0.7862 86 K 0.0795 0.0917 0.8289 87 A 0.0587 0.1460 0.7953 88 Q 0.0620 0.1475 0.7905 89 D 0.0975 0.1035 0.7990 90 T 0.1819 0.0859 0.7322 91 V 0.0836 0.0365 0.8799