# This file is the result of combining several RDB files, specifically # T0213.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0213.t2k.stride-ebghtl.rdb (weight 1.24869) # T0213.t2k.str2.rdb (weight 1.54758) # T0213.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 T0213.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0213 # 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 T0213.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 14 # # ============================================ # Comments from T0213.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0213 # 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 T0213.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 14 # # ============================================ # Comments from T0213.t2k.str2.rdb # ============================================ # TARGET T0213 # 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 T0213.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 14 # # ============================================ # Comments from T0213.t2k.alpha.rdb # ============================================ # TARGET T0213 # 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 T0213.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 14 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0646 0.0317 0.9037 2 Q 0.0892 0.0306 0.8802 3 P 0.0858 0.0778 0.8364 4 N 0.0790 0.1128 0.8081 5 D 0.2843 0.1288 0.5869 6 I 0.5654 0.1125 0.3221 7 T 0.5643 0.1159 0.3199 8 F 0.2640 0.4824 0.2537 9 F 0.1019 0.6809 0.2172 10 Q 0.0662 0.7600 0.1738 11 R 0.0581 0.7576 0.1843 12 F 0.0557 0.7363 0.2080 13 Q 0.0395 0.8497 0.1108 14 D 0.0228 0.8564 0.1208 15 D 0.0217 0.8338 0.1445 16 I 0.0274 0.8050 0.1676 17 L 0.0318 0.6648 0.3034 18 A 0.0397 0.3763 0.5840 19 G 0.0368 0.0815 0.8817 20 R 0.0727 0.0499 0.8774 21 K 0.1508 0.0393 0.8099 22 T 0.5224 0.0396 0.4380 23 I 0.6135 0.0211 0.3655 24 T 0.6477 0.0294 0.3229 25 I 0.5871 0.0725 0.3403 26 R 0.3063 0.0850 0.6087 27 D 0.1899 0.0835 0.7266 28 E 0.0815 0.2560 0.6626 29 S 0.0988 0.2430 0.6582 30 E 0.0553 0.5330 0.4117 31 S 0.0548 0.5534 0.3918 32 H 0.0894 0.3977 0.5129 33 F 0.2261 0.0815 0.6925 34 K 0.1287 0.0264 0.8448 35 T 0.0528 0.0950 0.8522 36 G 0.0355 0.0615 0.9030 37 D 0.2505 0.0247 0.7248 38 V 0.7909 0.0046 0.2046 39 L 0.8495 0.0061 0.1444 40 R 0.8858 0.0058 0.1083 41 V 0.8292 0.0104 0.1604 42 G 0.7744 0.0115 0.2140 43 R 0.6635 0.0139 0.3226 44 F 0.2631 0.0584 0.6785 45 E 0.1037 0.0974 0.7989 46 D 0.0626 0.0935 0.8439 47 D 0.0759 0.0683 0.8559 48 G 0.3597 0.0385 0.6018 49 Y 0.7047 0.0222 0.2731 50 F 0.7806 0.0152 0.2042 51 C 0.7539 0.0129 0.2333 52 T 0.7875 0.0070 0.2054 53 I 0.8741 0.0042 0.1217 54 E 0.9049 0.0041 0.0910 55 V 0.9185 0.0030 0.0785 56 T 0.8612 0.0156 0.1232 57 A 0.8622 0.0056 0.1322 58 T 0.7890 0.0107 0.2003 59 S 0.7576 0.0097 0.2328 60 T 0.7464 0.0066 0.2470 61 V 0.6731 0.0073 0.3196 62 T 0.4066 0.0108 0.5826 63 L 0.0733 0.4696 0.4570 64 D 0.0205 0.6045 0.3750 65 T 0.0307 0.6136 0.3556 66 L 0.0629 0.4914 0.4457 67 T 0.0645 0.4466 0.4890 68 E 0.0096 0.8831 0.1074 69 K 0.0057 0.9171 0.0772 70 H 0.0060 0.9218 0.0722 71 A 0.0057 0.9094 0.0850 72 E 0.0062 0.8925 0.1013 73 Q 0.0066 0.8353 0.1580 74 E 0.0326 0.5946 0.3728 75 N 0.0362 0.3710 0.5928 76 M 0.0510 0.2817 0.6673 77 T 0.0533 0.2384 0.7083 78 L 0.0057 0.8924 0.1019 79 T 0.0048 0.9457 0.0495 80 E 0.0047 0.9481 0.0472 81 L 0.0047 0.9538 0.0415 82 K 0.0047 0.9535 0.0418 83 K 0.0050 0.9488 0.0462 84 V 0.0050 0.9471 0.0479 85 I 0.0055 0.9445 0.0500 86 A 0.0059 0.9249 0.0692 87 D 0.0090 0.8450 0.1460 88 I 0.0254 0.6390 0.3355 89 Y 0.0949 0.0634 0.8417 90 P 0.0303 0.1030 0.8667 91 G 0.0598 0.0682 0.8720 92 Q 0.0780 0.2417 0.6803 93 T 0.0819 0.1672 0.7509 94 Q 0.4349 0.0669 0.4982 95 F 0.7722 0.0080 0.2198 96 Y 0.9048 0.0043 0.0910 97 V 0.9259 0.0034 0.0707 98 I 0.9202 0.0042 0.0756 99 E 0.9128 0.0045 0.0827 100 F 0.8802 0.0048 0.1151 101 K 0.8298 0.0055 0.1647 102 C 0.6737 0.0078 0.3185 103 L 0.0833 0.0245 0.8923