# This file is the result of combining several RDB files, specifically # T0224.t04.dssp-ebghstl.rdb (weight 1.53986) # T0224.t04.stride-ebghtl.rdb (weight 1.24869) # T0224.t04.str2.rdb (weight 1.54758) # T0224.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 T0224.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0224 # 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 T0224.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 16.5735 # # ============================================ # Comments from T0224.t04.stride-ebghtl.rdb # ============================================ # TARGET T0224 # 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 T0224.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 16.5735 # # ============================================ # Comments from T0224.t04.str2.rdb # ============================================ # TARGET T0224 # 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 T0224.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 16.5735 # # ============================================ # Comments from T0224.t04.alpha.rdb # ============================================ # TARGET T0224 # 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 T0224.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 16.5735 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2595 0.0410 0.6995 2 A 0.7118 0.0256 0.2627 3 L 0.8691 0.0172 0.1137 4 V 0.9036 0.0162 0.0803 5 L 0.8941 0.0161 0.0898 6 V 0.8271 0.0229 0.1500 7 K 0.5574 0.0228 0.4198 8 Y 0.1767 0.0300 0.7933 9 G 0.0595 0.0713 0.8692 10 T 0.0654 0.0594 0.8752 11 D 0.0573 0.0665 0.8763 12 H 0.0650 0.0433 0.8917 13 P 0.0777 0.1347 0.7876 14 V 0.0329 0.7589 0.2082 15 E 0.0329 0.8137 0.1534 16 K 0.0375 0.8240 0.1385 17 L 0.0754 0.7665 0.1581 18 K 0.0950 0.7254 0.1797 19 I 0.0935 0.7307 0.1757 20 R 0.0689 0.6520 0.2792 21 S 0.0899 0.4855 0.4245 22 A 0.1441 0.2048 0.6511 23 K 0.0826 0.1223 0.7950 24 A 0.0197 0.3782 0.6021 25 E 0.0393 0.1780 0.7827 26 D 0.1629 0.0893 0.7478 27 K 0.5746 0.0432 0.3821 28 I 0.9005 0.0122 0.0873 29 V 0.9131 0.0164 0.0704 30 L 0.8758 0.0306 0.0936 31 I 0.6673 0.0703 0.2624 32 Q 0.2610 0.1399 0.5992 33 N 0.1275 0.2067 0.6658 34 G 0.1778 0.4456 0.3766 35 V 0.2393 0.6241 0.1366 36 F 0.1988 0.7054 0.0958 37 W 0.1814 0.7117 0.1069 38 A 0.1785 0.6636 0.1578 39 L 0.1415 0.6380 0.2205 40 E 0.0988 0.5453 0.3559 41 E 0.0747 0.3205 0.6049 42 L 0.0966 0.0935 0.8099 43 E 0.0745 0.0653 0.8601 44 T 0.0852 0.0359 0.8789 45 P 0.0964 0.0594 0.8441 46 A 0.3058 0.0245 0.6696 47 K 0.6302 0.0234 0.3464 48 V 0.9013 0.0070 0.0918 49 Y 0.9186 0.0066 0.0748 50 A 0.8942 0.0130 0.0928 51 I 0.7353 0.0293 0.2355 52 K 0.1996 0.2592 0.5412 53 D 0.0545 0.3864 0.5591 54 D 0.0505 0.5186 0.4309 55 F 0.0574 0.6905 0.2521 56 L 0.0681 0.6664 0.2655 57 A 0.0856 0.6479 0.2665 58 R 0.0593 0.4751 0.4656 59 G 0.0542 0.1289 0.8169 60 Y 0.1114 0.0853 0.8033 61 S 0.1102 0.1448 0.7450 62 E 0.0760 0.2866 0.6373 63 E 0.0805 0.2600 0.6595 64 D 0.0855 0.2134 0.7012 65 S 0.0444 0.1748 0.7807 66 K 0.0803 0.0537 0.8661 67 V 0.1998 0.0133 0.7869 68 P 0.3582 0.0097 0.6321 69 L 0.8460 0.0086 0.1455 70 I 0.7918 0.0174 0.1908 71 T 0.6433 0.0092 0.3475 72 Y 0.1491 0.5370 0.3138 73 S 0.0309 0.7332 0.2359 74 E 0.0302 0.7784 0.1914 75 F 0.0559 0.8036 0.1404 76 I 0.0907 0.8237 0.0856 77 D 0.0902 0.8415 0.0683 78 L 0.1187 0.7895 0.0917 79 L 0.1633 0.6928 0.1440 80 E 0.1925 0.5510 0.2565 81 G 0.1808 0.3266 0.4926 82 E 0.1356 0.2884 0.5759 83 E 0.1191 0.3058 0.5752 84 K 0.1586 0.2882 0.5532 85 F 0.2530 0.2222 0.5248 86 I 0.2192 0.1114 0.6694 87 G 0.0829 0.0478 0.8693