# This file is the result of combining several RDB files, specifically # T0272.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0272.t2k.stride-ebghtl.rdb (weight 1.24869) # T0272.t2k.str2.rdb (weight 1.54758) # T0272.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 T0272.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0272 # 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 T0272.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 17 # # ============================================ # Comments from T0272.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0272 # 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 T0272.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 17 # # ============================================ # Comments from T0272.t2k.str2.rdb # ============================================ # TARGET T0272 # 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 T0272.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 17 # # ============================================ # Comments from T0272.t2k.alpha.rdb # ============================================ # TARGET T0272 # 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 T0272.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 17 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0440 0.0849 0.8711 2 T 0.0823 0.1438 0.7739 3 G 0.0648 0.1742 0.7610 4 K 0.0748 0.2066 0.7187 5 R 0.1251 0.2519 0.6230 6 V 0.1129 0.2969 0.5902 7 A 0.0790 0.4254 0.4956 8 L 0.0599 0.6060 0.3341 9 K 0.0427 0.6560 0.3014 10 T 0.0354 0.6707 0.2939 11 P 0.0105 0.8633 0.1262 12 A 0.0077 0.9007 0.0916 13 E 0.0061 0.9259 0.0680 14 K 0.0055 0.9309 0.0636 15 V 0.0050 0.9431 0.0519 16 A 0.0049 0.9429 0.0522 17 W 0.0048 0.9461 0.0491 18 L 0.0049 0.9409 0.0542 19 E 0.0050 0.9286 0.0664 20 R 0.0058 0.9108 0.0834 21 R 0.0060 0.8928 0.1012 22 L 0.0073 0.8736 0.1191 23 E 0.0090 0.8326 0.1584 24 E 0.0136 0.7037 0.2827 25 G 0.0474 0.3046 0.6481 26 G 0.0539 0.0351 0.9111 27 F 0.2584 0.0165 0.7252 28 R 0.6691 0.0139 0.3171 29 L 0.7045 0.0295 0.2660 30 L 0.5896 0.0714 0.3390 31 E 0.3755 0.1406 0.4840 32 G 0.2029 0.1716 0.6255 33 E 0.1848 0.1175 0.6977 34 R 0.1281 0.1269 0.7450 35 G 0.1077 0.1107 0.7816 36 P 0.0374 0.5845 0.3781 37 W 0.0401 0.6248 0.3351 38 V 0.0524 0.6634 0.2842 39 Q 0.0645 0.6430 0.2926 40 I 0.0649 0.6489 0.2862 41 L 0.0494 0.6511 0.2995 42 Q 0.0536 0.5717 0.3747 43 D 0.0762 0.5414 0.3823 44 T 0.0847 0.5961 0.3192 45 F 0.0789 0.6085 0.3126 46 L 0.0665 0.6418 0.2916 47 E 0.0871 0.6322 0.2807 48 V 0.1152 0.6044 0.2804 49 R 0.1599 0.5180 0.3221 50 R 0.1918 0.4060 0.4022 51 K 0.2188 0.3474 0.4338 52 K 0.2767 0.2850 0.4383 53 D 0.3080 0.2270 0.4650 54 G 0.2390 0.1947 0.5663 55 E 0.1028 0.1963 0.7009 56 E 0.0707 0.1457 0.7836 57 A 0.0824 0.0975 0.8201 58 G 0.1233 0.0523 0.8244 59 K 0.4337 0.0145 0.5518 60 L 0.7291 0.0063 0.2646 61 L 0.8601 0.0050 0.1349 62 Q 0.8931 0.0043 0.1026 63 V 0.8541 0.0056 0.1403 64 Q 0.8306 0.0151 0.1543 65 A 0.8684 0.0064 0.1252 66 V 0.8750 0.0047 0.1203 67 L 0.8607 0.0057 0.1336 68 F 0.8242 0.0162 0.1596 69 E 0.7159 0.0364 0.2478 70 G 0.7411 0.0136 0.2453 71 R 0.8328 0.0099 0.1573 72 L 0.8718 0.0092 0.1190 73 E 0.8743 0.0051 0.1206 74 V 0.6983 0.0150 0.2867 75 V 0.2868 0.0255 0.6877 76 D 0.1675 0.0129 0.8196 77 P 0.0063 0.8467 0.1470 78 E 0.0053 0.9312 0.0635 79 R 0.0050 0.9489 0.0461 80 A 0.0048 0.9543 0.0409 81 L 0.0048 0.9543 0.0408 82 A 0.0051 0.9494 0.0455 83 T 0.0054 0.9430 0.0516 84 L 0.0074 0.9271 0.0656 85 R 0.0087 0.8588 0.1325 86 R 0.0231 0.6066 0.3703 87 G 0.0319 0.3232 0.6448 88 V 0.0794 0.2281 0.6925 89 G 0.0772 0.1827 0.7401 90 P 0.0557 0.4034 0.5409 91 G 0.0746 0.4919 0.4335 92 K 0.1467 0.4742 0.3791 93 A 0.2237 0.3560 0.4204 94 L 0.1818 0.2441 0.5741 95 G 0.1708 0.1542 0.6750 96 L 0.1962 0.1937 0.6101 97 G 0.2297 0.2139 0.5564 98 L 0.3037 0.3452 0.3511 99 L 0.4049 0.2882 0.3068 100 S 0.4493 0.2119 0.3388 101 V 0.3677 0.0769 0.5554 102 A 0.1858 0.0287 0.7855 103 P 0.0579 0.0233 0.9188