# This file is the result of combining several RDB files, specifically # T0319.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0319.t2k.stride-ebghtl.rdb (weight 1.24869) # T0319.t2k.str2.rdb (weight 1.54758) # T0319.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 T0319.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0319 # 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 T0319.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 55 # # ============================================ # Comments from T0319.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0319 # 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 T0319.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 55 # # ============================================ # Comments from T0319.t2k.str2.rdb # ============================================ # TARGET T0319 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0319.t2k-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 20.7512 # # ============================================ # Comments from T0319.t2k.alpha.rdb # ============================================ # TARGET T0319 # 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 T0319.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 55 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0607 0.0823 0.8570 2 K 0.2714 0.1611 0.5675 3 F 0.5790 0.1401 0.2809 4 L 0.6389 0.1569 0.2043 5 T 0.6547 0.1273 0.2180 6 T 0.5171 0.2365 0.2464 7 N 0.3731 0.2530 0.3740 8 F 0.3304 0.3564 0.3133 9 L 0.3931 0.2751 0.3318 10 K 0.4011 0.2393 0.3596 11 C 0.2665 0.2832 0.4503 12 S 0.1992 0.3207 0.4801 13 V 0.2739 0.2889 0.4372 14 K 0.2607 0.2213 0.5180 15 A 0.2662 0.1122 0.6216 16 C 0.3397 0.0627 0.5976 17 D 0.2825 0.0546 0.6628 18 T 0.2153 0.0802 0.7045 19 S 0.1012 0.0754 0.8234 20 N 0.0856 0.0662 0.8482 21 D 0.1615 0.0424 0.7961 22 N 0.3421 0.0495 0.6084 23 F 0.5581 0.0261 0.4158 24 P 0.6965 0.0210 0.2825 25 L 0.7334 0.0261 0.2405 26 Q 0.6902 0.0344 0.2754 27 Y 0.5033 0.1730 0.3238 28 D 0.3545 0.2366 0.4089 29 G 0.3002 0.2893 0.4105 30 S 0.2732 0.2948 0.4320 31 K 0.2994 0.2700 0.4306 32 C 0.1989 0.4483 0.3528 33 Q 0.2070 0.3952 0.3977 34 L 0.2176 0.3653 0.4171 35 V 0.2953 0.2645 0.4402 36 Q 0.3972 0.2101 0.3927 37 D 0.3675 0.2031 0.4294 38 E 0.2668 0.1644 0.5688 39 S 0.1995 0.1765 0.6240 40 I 0.2264 0.1737 0.5999 41 E 0.2610 0.1398 0.5992 42 F 0.2050 0.1134 0.6817 43 N 0.0960 0.0526 0.8514 44 P 0.0054 0.8972 0.0973 45 E 0.0052 0.9259 0.0689 46 F 0.0050 0.9378 0.0572 47 L 0.0062 0.9382 0.0556 48 L 0.0057 0.8901 0.1042 49 N 0.0068 0.8072 0.1860 50 I 0.0135 0.7475 0.2390 51 V 0.0282 0.6191 0.3527 52 D 0.0142 0.5570 0.4289 53 R 0.0251 0.5501 0.4248 54 V 0.0900 0.2931 0.6169 55 D 0.0642 0.2956 0.6403 56 W 0.0071 0.9305 0.0624 57 P 0.0048 0.9543 0.0410 58 A 0.0047 0.9589 0.0364 59 V 0.0047 0.9594 0.0359 60 L 0.0047 0.9598 0.0356 61 T 0.0047 0.9578 0.0375 62 V 0.0047 0.9556 0.0397 63 A 0.0048 0.9513 0.0439 64 A 0.0050 0.9278 0.0672 65 E 0.0057 0.8578 0.1366 66 L 0.0441 0.4620 0.4938 67 G 0.0384 0.1667 0.7949 68 N 0.0531 0.2512 0.6957 69 N 0.0519 0.2756 0.6724 70 A 0.0958 0.2004 0.7039 71 L 0.1205 0.0693 0.8102 72 P 0.0707 0.0811 0.8482 73 P 0.0394 0.2449 0.7157 74 T 0.0465 0.2433 0.7102 75 K 0.0657 0.1239 0.8103 76 P 0.0430 0.1785 0.7785 77 S 0.0657 0.1562 0.7781 78 F 0.0824 0.1034 0.8142 79 P 0.0817 0.1150 0.8033 80 S 0.0427 0.2922 0.6652 81 S 0.0553 0.2801 0.6646 82 I 0.0778 0.2936 0.6285 83 Q 0.0672 0.3474 0.5854 84 E 0.0358 0.3797 0.5845 85 L 0.0535 0.3077 0.6388 86 T 0.0322 0.3991 0.5687 87 D 0.0250 0.5783 0.3966 88 D 0.0235 0.5677 0.4088 89 D 0.0223 0.5637 0.4141 90 M 0.0056 0.9165 0.0780 91 A 0.0047 0.9427 0.0526 92 I 0.0048 0.9482 0.0471 93 L 0.0047 0.9556 0.0397 94 N 0.0047 0.9564 0.0389 95 D 0.0048 0.9510 0.0443 96 L 0.0049 0.9483 0.0469 97 H 0.0053 0.9475 0.0472 98 T 0.0061 0.9364 0.0576 99 L 0.0075 0.9347 0.0578 100 L 0.0211 0.9000 0.0789 101 L 0.0526 0.8090 0.1384 102 Q 0.1501 0.6522 0.1977 103 T 0.1880 0.4377 0.3744 104 S 0.3781 0.2793 0.3427 105 I 0.5471 0.1710 0.2819 106 A 0.5613 0.1449 0.2938 107 E 0.4952 0.1063 0.3985 108 G 0.4408 0.0552 0.5040 109 E 0.6765 0.0249 0.2985 110 M 0.8019 0.0128 0.1853 111 K 0.7564 0.0116 0.2320 112 C 0.5112 0.0198 0.4690 113 R 0.0650 0.1533 0.7817 114 N 0.0333 0.1374 0.8292 115 C 0.1100 0.0831 0.8069 116 G 0.1461 0.0370 0.8169 117 H 0.3752 0.0179 0.6069 118 I 0.7406 0.0109 0.2484 119 Y 0.7016 0.0162 0.2822 120 Y 0.6486 0.0238 0.3276 121 I 0.4898 0.0715 0.4387 122 K 0.2615 0.1144 0.6241 123 N 0.0911 0.1032 0.8057 124 G 0.0729 0.0806 0.8465 125 I 0.2048 0.0512 0.7440 126 P 0.2659 0.0814 0.6527 127 N 0.2980 0.1440 0.5580 128 L 0.3304 0.1581 0.5115 129 L 0.2442 0.1271 0.6287 130 L 0.1299 0.0356 0.8345 131 P 0.0759 0.0442 0.8799 132 P 0.0273 0.6016 0.3711 133 H 0.0401 0.6120 0.3479 134 L 0.1013 0.5527 0.3460 135 V 0.1004 0.2205 0.6791