# This file is the result of combining several RDB files, specifically # T0471.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0471.t2k.stride-ebghtl.rdb (weight 1.24869) # T0471.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 T0471.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0471 # 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 T0471.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 24 # # ============================================ # Comments from T0471.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0471 # 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 T0471.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 24 # # ============================================ # Comments from T0471.t2k.str.rdb # ============================================ # TARGET T0471 # 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 T0471.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 24 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0145 0.0331 0.9523 2 W 0.0686 0.1993 0.7322 3 N 0.0671 0.2995 0.6334 4 D 0.0309 0.6559 0.3132 5 L 0.0318 0.7421 0.2261 6 A 0.0504 0.7533 0.1962 7 V 0.0872 0.7680 0.1448 8 Y 0.1201 0.7580 0.1219 9 I 0.1583 0.7390 0.1027 10 I 0.1647 0.7399 0.0953 11 R 0.1719 0.7067 0.1214 12 C 0.1753 0.6065 0.2182 13 S 0.1587 0.3524 0.4889 14 G 0.0728 0.1018 0.8254 15 P 0.0439 0.0578 0.8983 16 G 0.0653 0.0422 0.8925 17 T 0.2834 0.0185 0.6981 18 R 0.7112 0.0039 0.2849 19 V 0.9357 0.0024 0.0619 20 V 0.9616 0.0024 0.0360 21 E 0.9702 0.0024 0.0274 22 V 0.9141 0.0027 0.0832 23 G 0.7600 0.0070 0.2330 24 A 0.3671 0.0206 0.6123 25 G 0.1422 0.0439 0.8140 26 R 0.1059 0.0894 0.8046 27 F 0.0841 0.1663 0.7495 28 L 0.0093 0.8327 0.1580 29 Y 0.0063 0.9013 0.0925 30 V 0.0037 0.9649 0.0314 31 S 0.0037 0.9713 0.0250 32 D 0.0037 0.9678 0.0285 33 Y 0.0037 0.9661 0.0302 34 I 0.0037 0.9668 0.0294 35 R 0.0037 0.9508 0.0454 36 K 0.0038 0.8690 0.1272 37 H 0.0053 0.4780 0.5167 38 S 0.0135 0.0172 0.9693 39 K 0.0598 0.0126 0.9277 40 V 0.6010 0.0077 0.3913 41 D 0.9199 0.0030 0.0771 42 L 0.9650 0.0025 0.0325 43 V 0.9640 0.0031 0.0328 44 L 0.9282 0.0043 0.0675 45 T 0.7759 0.0081 0.2159 46 D 0.4661 0.0270 0.5069 47 I 0.3555 0.0428 0.6017 48 K 0.1504 0.0499 0.7996 49 P 0.0638 0.0916 0.8445 50 S 0.0359 0.0901 0.8740 51 H 0.0663 0.0595 0.8741 52 G 0.2108 0.0271 0.7621 53 G 0.4343 0.0228 0.5429 54 I 0.7491 0.0276 0.2234 55 V 0.7955 0.0373 0.1672 56 R 0.7586 0.0669 0.1745 57 D 0.5292 0.1033 0.3675 58 D 0.2610 0.1172 0.6218 59 I 0.1639 0.1406 0.6955 60 T 0.1135 0.1181 0.7684 61 S 0.0536 0.0383 0.9081 62 P 0.0425 0.1018 0.8557 63 R 0.0627 0.1331 0.8042 64 M 0.0260 0.6424 0.3316 65 E 0.0491 0.6790 0.2719 66 I 0.0412 0.7815 0.1772 67 Y 0.0735 0.7076 0.2188 68 R 0.0554 0.4957 0.4489 69 G 0.0705 0.2422 0.6873 70 A 0.1282 0.1211 0.7508 71 A 0.2898 0.0769 0.6334 72 L 0.8525 0.0574 0.0901 73 I 0.9016 0.0467 0.0517 74 Y 0.8974 0.0480 0.0546 75 S 0.7787 0.0545 0.1668 76 I 0.4364 0.0381 0.5254 77 R 0.1186 0.0192 0.8621 78 P 0.0466 0.0151 0.9383 79 P 0.0223 0.1504 0.8272 80 A 0.0049 0.7445 0.2506 81 E 0.0050 0.7839 0.2111 82 I 0.0075 0.7694 0.2231 83 H 0.0093 0.7355 0.2552 84 S 0.0055 0.8439 0.1506 85 S 0.0041 0.9163 0.0797 86 L 0.0039 0.9604 0.0358 87 M 0.0038 0.9654 0.0308 88 R 0.0038 0.9650 0.0312 89 V 0.0037 0.9681 0.0282 90 A 0.0037 0.9582 0.0380 91 D 0.0038 0.8963 0.1000 92 A 0.0039 0.8065 0.1896 93 V 0.0201 0.4575 0.5224 94 G 0.0164 0.0132 0.9704 95 A 0.0562 0.0069 0.9370 96 R 0.2188 0.0065 0.7747 97 L 0.9288 0.0025 0.0687 98 I 0.9749 0.0024 0.0227 99 I 0.9699 0.0027 0.0274 100 K 0.8995 0.0042 0.0963 101 P 0.5305 0.0102 0.4593 102 L 0.1464 0.0374 0.8162 103 T 0.0756 0.0625 0.8619 104 G 0.0556 0.0817 0.8627 105 E 0.1464 0.1014 0.7521 106 D 0.2440 0.1006 0.6554 107 I 0.2031 0.1405 0.6564 108 V 0.1821 0.1946 0.6232 109 T 0.1639 0.1899 0.6462 110 E 0.2033 0.1269 0.6698 111 R 0.3552 0.0519 0.5929 112 K 0.5637 0.0298 0.4064 113 M 0.6568 0.0288 0.3143 114 K 0.6722 0.0317 0.2960 115 L 0.5822 0.0261 0.3916 116 V 0.4201 0.0241 0.5558 117 N 0.2097 0.0198 0.7704 118 Y 0.2041 0.0273 0.7687 119 G 0.4202 0.0268 0.5530 120 R 0.7437 0.0179 0.2384 121 T 0.8806 0.0113 0.1081 122 Y 0.9435 0.0075 0.0490 123 F 0.9403 0.0098 0.0500 124 Y 0.9166 0.0142 0.0692 125 E 0.8597 0.0224 0.1179 126 Y 0.7533 0.0519 0.1948 127 I 0.6021 0.0774 0.3206 128 A 0.4968 0.1008 0.4024 129 E 0.3600 0.0824 0.5576 130 V 0.2541 0.0739 0.6720 131 R 0.2265 0.0817 0.6918 132 S 0.0986 0.0683 0.8331 133 R 0.0105 0.0048 0.9847