# This file is the result of combining several RDB files, specifically # T0243.t04.dssp-ebghstl.rdb (weight 1.53986) # T0243.t04.stride-ebghtl.rdb (weight 1.24869) # T0243.t04.str2.rdb (weight 1.54758) # T0243.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 T0243.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0243 # 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 T0243.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 1 # # ============================================ # Comments from T0243.t04.stride-ebghtl.rdb # ============================================ # TARGET T0243 # 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 T0243.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 1 # # ============================================ # Comments from T0243.t04.str2.rdb # ============================================ # TARGET T0243 # 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 T0243.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 1 # # ============================================ # Comments from T0243.t04.alpha.rdb # ============================================ # TARGET T0243 # 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 T0243.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2070 0.2002 0.5928 2 K 0.3752 0.2318 0.3930 3 I 0.3809 0.3468 0.2723 4 R 0.3662 0.3341 0.2996 5 K 0.3947 0.3582 0.2471 6 Y 0.3914 0.3634 0.2451 7 M 0.4344 0.3054 0.2603 8 R 0.4699 0.2556 0.2746 9 I 0.4440 0.2997 0.2563 10 N 0.3911 0.2803 0.3286 11 Y 0.5808 0.2316 0.1876 12 Y 0.7197 0.1714 0.1089 13 I 0.8377 0.0792 0.0831 14 I 0.8585 0.0550 0.0866 15 L 0.8534 0.0435 0.1031 16 K 0.8413 0.0542 0.1045 17 V 0.8510 0.0555 0.0935 18 L 0.8321 0.0764 0.0916 19 V 0.8039 0.0854 0.1107 20 I 0.6850 0.0932 0.2218 21 N 0.1802 0.0767 0.7431 22 G 0.0499 0.0985 0.8515 23 S 0.1159 0.2183 0.6658 24 R 0.1717 0.4052 0.4231 25 L 0.1093 0.5402 0.3505 26 E 0.0903 0.5562 0.3535 27 K 0.0570 0.6964 0.2466 28 K 0.0407 0.7521 0.2073 29 R 0.0421 0.7431 0.2148 30 L 0.0383 0.7398 0.2219 31 R 0.0235 0.8143 0.1622 32 S 0.0121 0.9074 0.0805 33 E 0.0122 0.9079 0.0799 34 I 0.0168 0.8993 0.0838 35 L 0.0364 0.8453 0.1183 36 K 0.0501 0.7502 0.1997 37 R 0.0732 0.5896 0.3372 38 F 0.1375 0.2628 0.5997 39 D 0.2236 0.0673 0.7091 40 I 0.3443 0.0393 0.6164 41 D 0.4191 0.0277 0.5532 42 I 0.2134 0.1887 0.5979 43 S 0.1082 0.2097 0.6821 44 D 0.0492 0.1658 0.7851 45 G 0.0906 0.1015 0.8079 46 V 0.4053 0.1054 0.4893 47 L 0.5368 0.1509 0.3123 48 Y 0.2876 0.3627 0.3497 49 P 0.1578 0.5296 0.3126 50 L 0.0753 0.6970 0.2276 51 I 0.0408 0.8058 0.1534 52 D 0.0266 0.8255 0.1480 53 S 0.0196 0.8219 0.1585 54 L 0.0312 0.7661 0.2027 55 I 0.0453 0.6861 0.2685 56 D 0.0459 0.5621 0.3919 57 D 0.0348 0.5575 0.4078 58 K 0.0603 0.5784 0.3613 59 I 0.1710 0.4807 0.3483 60 L 0.2435 0.3456 0.4108 61 R 0.2299 0.2756 0.4945 62 E 0.1647 0.3913 0.4439 63 E 0.1829 0.3045 0.5126 64 E 0.2582 0.1754 0.5663 65 A 0.0952 0.0310 0.8738 66 P 0.0513 0.0789 0.8697 67 D 0.0449 0.0473 0.9079 68 G 0.0958 0.0378 0.8664 69 K 0.3994 0.0153 0.5853 70 V 0.8762 0.0056 0.1181 71 L 0.8917 0.0104 0.0980 72 F 0.8935 0.0126 0.0939 73 L 0.8317 0.0205 0.1478 74 T 0.5931 0.0490 0.3578 75 E 0.2329 0.2398 0.5273 76 K 0.0862 0.2529 0.6609 77 G 0.0588 0.2248 0.7164 78 M 0.0811 0.4151 0.5038 79 K 0.0691 0.6428 0.2881 80 E 0.0537 0.7053 0.2410 81 F 0.0174 0.8609 0.1218 82 E 0.0102 0.9287 0.0611 83 E 0.0113 0.9287 0.0601 84 L 0.0096 0.9255 0.0649 85 H 0.0104 0.9283 0.0613 86 E 0.0077 0.9318 0.0605 87 F 0.0119 0.9130 0.0751 88 F 0.0196 0.8796 0.1009 89 K 0.0297 0.8463 0.1240 90 K 0.0646 0.7921 0.1433 91 I 0.1119 0.6505 0.2376 92 V 0.1485 0.3022 0.5494 93 C 0.0816 0.0653 0.8531