# This file is the result of combining several RDB files, specifically # T0581.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0581.t2k.stride-ebghtl.rdb (weight 1.24869) # T0581.t2k.str2.rdb (weight 1.54758) # T0581.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 T0581.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0581 # 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 T0581.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 11 # # ============================================ # Comments from T0581.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0581 # 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 T0581.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 11 # # ============================================ # Comments from T0581.t2k.str2.rdb # ============================================ # TARGET T0581 # 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 T0581.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 11 # # ============================================ # Comments from T0581.t2k.alpha.rdb # ============================================ # TARGET T0581 # 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 T0581.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 11 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0540 0.1173 0.8286 2 S 0.1281 0.3166 0.5553 3 R 0.0856 0.4888 0.4256 4 F 0.0288 0.7529 0.2183 5 M 0.0099 0.8695 0.1207 6 A 0.0081 0.8818 0.1100 7 L 0.0080 0.9309 0.0611 8 A 0.0083 0.9259 0.0658 9 L 0.0069 0.9228 0.0703 10 C 0.0074 0.8991 0.0935 11 F 0.0084 0.7964 0.1952 12 V 0.0108 0.7175 0.2717 13 L 0.0194 0.6691 0.3116 14 P 0.0086 0.8607 0.1307 15 T 0.0065 0.9140 0.0795 16 A 0.0057 0.9173 0.0770 17 A 0.0062 0.9074 0.0864 18 H 0.0064 0.8829 0.1107 19 A 0.0085 0.8091 0.1824 20 A 0.0182 0.6680 0.3138 21 S 0.0383 0.5776 0.3841 22 L 0.0084 0.8004 0.1912 23 K 0.0110 0.8631 0.1259 24 D 0.0058 0.9080 0.0861 25 F 0.0076 0.9061 0.0863 26 E 0.0073 0.9132 0.0794 27 L 0.0053 0.9170 0.0777 28 S 0.0063 0.9332 0.0604 29 K 0.0056 0.9409 0.0535 30 M 0.0061 0.9470 0.0469 31 L 0.0051 0.9487 0.0462 32 E 0.0054 0.9506 0.0440 33 K 0.0053 0.9460 0.0487 34 V 0.0051 0.9440 0.0509 35 A 0.0058 0.9318 0.0623 36 K 0.0062 0.8845 0.1092 37 E 0.0124 0.7858 0.2019 38 S 0.0503 0.4319 0.5177 39 S 0.0373 0.1890 0.7737 40 V 0.0478 0.0971 0.8550 41 G 0.0429 0.0784 0.8787 42 T 0.0592 0.0754 0.8654 43 P 0.0537 0.3533 0.5930 44 R 0.1111 0.4254 0.4634 45 A 0.1854 0.4738 0.3408 46 I 0.2447 0.3377 0.4176 47 N 0.1592 0.2894 0.5514 48 E 0.0645 0.4633 0.4722 49 D 0.0737 0.4626 0.4637 50 I 0.0409 0.6478 0.3113 51 L 0.0607 0.5722 0.3671 52 D 0.0681 0.4425 0.4895 53 Q 0.1049 0.3058 0.5892 54 G 0.1454 0.2479 0.6068 55 Y 0.3331 0.2460 0.4209 56 T 0.3883 0.2166 0.3951 57 V 0.3042 0.2901 0.4057 58 E 0.1735 0.2450 0.5815 59 G 0.0796 0.3809 0.5395 60 N 0.0928 0.5251 0.3821 61 Q 0.2574 0.4659 0.2767 62 L 0.3362 0.4604 0.2034 63 I 0.2552 0.4699 0.2750 64 N 0.2161 0.4875 0.2964 65 H 0.1793 0.4437 0.3770 66 L 0.2455 0.3398 0.4147 67 S 0.3892 0.1791 0.4318 68 V 0.2842 0.1477 0.5680 69 R 0.1310 0.1006 0.7684 70 A 0.0107 0.8666 0.1227 71 S 0.0074 0.9120 0.0807 72 H 0.0060 0.9272 0.0669 73 A 0.0049 0.9515 0.0436 74 E 0.0059 0.9487 0.0454 75 R 0.0056 0.9270 0.0674 76 M 0.0084 0.8995 0.0921 77 R 0.0117 0.8680 0.1203 78 S 0.0195 0.7626 0.2179 79 N 0.0752 0.4433 0.4815 80 P 0.0066 0.9183 0.0751 81 D 0.0055 0.9348 0.0596 82 S 0.0058 0.9399 0.0543 83 V 0.0054 0.9493 0.0453 84 R 0.0071 0.9391 0.0538 85 S 0.0093 0.9196 0.0712 86 Q 0.0122 0.8530 0.1347 87 L 0.0351 0.7703 0.1946 88 G 0.0291 0.7776 0.1933 89 D 0.0243 0.7545 0.2212 90 S 0.0408 0.7435 0.2157 91 V 0.0442 0.7065 0.2494 92 C 0.0488 0.5117 0.4395 93 S 0.0322 0.2705 0.6973 94 N 0.0494 0.3001 0.6504 95 T 0.0273 0.6728 0.2999 96 G 0.0236 0.7575 0.2189 97 Y 0.0127 0.9125 0.0749 98 R 0.0105 0.9160 0.0735 99 Q 0.0135 0.9273 0.0592 100 L 0.0136 0.9159 0.0705 101 L 0.0243 0.8521 0.1236 102 A 0.0429 0.7107 0.2464 103 R 0.0614 0.2548 0.6838 104 G 0.1118 0.0544 0.8338 105 A 0.3162 0.0369 0.6469 106 I 0.7323 0.0136 0.2541 107 L 0.8615 0.0107 0.1277 108 T 0.8933 0.0121 0.0946 109 Y 0.8688 0.0126 0.1187 110 S 0.7942 0.0203 0.1855 111 F 0.6475 0.0271 0.3255 112 T 0.5394 0.0423 0.4182 113 E 0.5547 0.0539 0.3914 114 Y 0.4677 0.0764 0.4559 115 K 0.3524 0.0830 0.5646 116 T 0.2720 0.0678 0.6602 117 N 0.1794 0.0653 0.7553 118 Q 0.2407 0.0393 0.7200 119 P 0.3962 0.0780 0.5257 120 V 0.3323 0.1856 0.4821 121 A 0.3532 0.1869 0.4599 122 T 0.3054 0.2621 0.4326 123 E 0.2209 0.5140 0.2651 124 R 0.1921 0.5528 0.2551 125 F 0.2373 0.4647 0.2979 126 D 0.1657 0.4594 0.3749 127 A 0.1011 0.4794 0.4196 128 G 0.1076 0.3003 0.5921 129 S 0.1104 0.1386 0.7510 130 C 0.1290 0.0814 0.7896 131 R 0.0994 0.1827 0.7179 132 I 0.0858 0.2083 0.7059 133 Q 0.0949 0.1635 0.7416 134 G 0.1135 0.1031 0.7834 135 K 0.1571 0.0920 0.7509 136 K 0.0581 0.0404 0.9014