# This file is the result of combining several RDB files, specifically # T0360.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0360.t2k.stride-ebghtl.rdb (weight 1.24869) # T0360.t2k.str2.rdb (weight 1.54758) # T0360.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 T0360.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0360 # 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 T0360.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 51 # # ============================================ # Comments from T0360.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0360 # 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 T0360.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 51 # # ============================================ # Comments from T0360.t2k.str2.rdb # ============================================ # TARGET T0360 # 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 T0360.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 51 # # ============================================ # Comments from T0360.t2k.alpha.rdb # ============================================ # TARGET T0360 # 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 T0360.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 51 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0747 0.0385 0.8868 2 T 0.0898 0.0612 0.8489 3 Q 0.0579 0.3676 0.5745 4 E 0.0399 0.3799 0.5802 5 T 0.0505 0.3772 0.5723 6 A 0.0427 0.5163 0.4410 7 L 0.0291 0.5607 0.4102 8 G 0.0213 0.6339 0.3448 9 A 0.0166 0.7245 0.2589 10 A 0.0147 0.7414 0.2439 11 L 0.0179 0.7184 0.2637 12 K 0.0252 0.6316 0.3432 13 S 0.0362 0.4898 0.4740 14 A 0.0544 0.3927 0.5529 15 V 0.0584 0.2880 0.6536 16 Q 0.0591 0.3313 0.6096 17 T 0.0624 0.2732 0.6644 18 M 0.0427 0.4667 0.4906 19 S 0.0378 0.5490 0.4132 20 K 0.0167 0.8020 0.1813 21 K 0.0075 0.9131 0.0795 22 K 0.0077 0.9244 0.0679 23 Q 0.0079 0.9360 0.0561 24 T 0.0084 0.9408 0.0508 25 E 0.0083 0.9393 0.0524 26 M 0.0073 0.9334 0.0593 27 I 0.0074 0.9144 0.0782 28 A 0.0105 0.8503 0.1392 29 D 0.0219 0.6720 0.3061 30 H 0.0400 0.3979 0.5621 31 I 0.0597 0.1976 0.7427 32 Y 0.0664 0.2366 0.6969 33 G 0.0595 0.3380 0.6025 34 K 0.0721 0.3338 0.5942 35 Y 0.0971 0.2548 0.6481 36 D 0.1012 0.1963 0.7025 37 V 0.0860 0.1425 0.7715 38 F 0.0525 0.1561 0.7914 39 K 0.0560 0.1287 0.8153 40 R 0.0819 0.0794 0.8387 41 F 0.1296 0.0682 0.8023 42 K 0.1466 0.0723 0.7811 43 P 0.1461 0.1599 0.6940 44 L 0.1952 0.2484 0.5564 45 A 0.2950 0.3390 0.3660 46 L 0.3474 0.3457 0.3069 47 G 0.2799 0.3325 0.3876 48 I 0.1196 0.5674 0.3131 49 D 0.0184 0.8979 0.0836 50 Q 0.0095 0.9310 0.0596 51 D 0.0081 0.9404 0.0515 52 L 0.0084 0.9325 0.0591 53 I 0.0072 0.8931 0.0997 54 A 0.0079 0.7445 0.2476 55 A 0.0151 0.5790 0.4059 56 L 0.0348 0.4288 0.5365 57 P 0.0110 0.4323 0.5567 58 Q 0.0172 0.3285 0.6543 59 Y 0.0856 0.1318 0.7827 60 D 0.0663 0.0957 0.8379 61 A 0.0054 0.9265 0.0682 62 A 0.0048 0.9463 0.0489 63 L 0.0048 0.9516 0.0436 64 I 0.0048 0.9561 0.0391 65 A 0.0047 0.9598 0.0355 66 R 0.0047 0.9575 0.0378 67 V 0.0047 0.9561 0.0392 68 L 0.0048 0.9527 0.0425 69 A 0.0050 0.9405 0.0545 70 N 0.0063 0.8872 0.1065 71 H 0.0113 0.7823 0.2064 72 C 0.0395 0.5498 0.4107 73 R 0.0334 0.2438 0.7228 74 R 0.0606 0.1902 0.7492 75 P 0.0250 0.7016 0.2735 76 R 0.0310 0.7947 0.1743 77 Y 0.0616 0.8346 0.1038 78 L 0.1112 0.7967 0.0922 79 K 0.1353 0.7739 0.0909 80 A 0.1439 0.7338 0.1223 81 L 0.1422 0.6816 0.1762 82 A 0.1284 0.5288 0.3427 83 R 0.0445 0.2174 0.7381 84 G 0.0410 0.0347 0.9243 85 G 0.1182 0.0166 0.8652 86 K 0.3129 0.0168 0.6703 87 R 0.6431 0.0168 0.3401 88 F 0.7515 0.0116 0.2369 89 D 0.4199 0.0162 0.5638 90 L 0.0972 0.0918 0.8109 91 N 0.0437 0.0304 0.9259 92 N 0.0396 0.0369 0.9235 93 R 0.1265 0.0216 0.8519 94 F 0.3550 0.0400 0.6050 95 K 0.2768 0.0850 0.6382 96 G 0.2453 0.1025 0.6522 97 E 0.3105 0.0678 0.6217 98 V 0.2774 0.0353 0.6874 99 T 0.0982 0.0336 0.8682 100 P 0.0051 0.9313 0.0636 101 E 0.0048 0.9427 0.0525 102 E 0.0048 0.9502 0.0450 103 Q 0.0047 0.9582 0.0371 104 A 0.0048 0.9558 0.0394 105 I 0.0050 0.9521 0.0430 106 A 0.0054 0.9501 0.0445 107 Q 0.0059 0.9432 0.0509 108 N 0.0072 0.9120 0.0808 109 H 0.0091 0.8862 0.1047 110 P 0.0073 0.8781 0.1146 111 F 0.0086 0.8399 0.1515 112 V 0.0087 0.8232 0.1681 113 Q 0.0179 0.7815 0.2007 114 Q 0.0119 0.8046 0.1834 115 A 0.0109 0.7995 0.1896 116 L 0.0101 0.8375 0.1524 117 Q 0.0100 0.8420 0.1480 118 Q 0.0085 0.8684 0.1231 119 Q 0.0108 0.8620 0.1272 120 S 0.0098 0.8506 0.1395 121 A 0.0098 0.8622 0.1280 122 Q 0.0114 0.8591 0.1295 123 A 0.0088 0.8643 0.1269 124 A 0.0090 0.8379 0.1531 125 A 0.0100 0.8345 0.1555 126 E 0.0112 0.7903 0.1985 127 T 0.0131 0.7405 0.2464 128 L 0.0196 0.6946 0.2858 129 S 0.0148 0.6983 0.2869 130 V 0.0144 0.7423 0.2434 131 E 0.0129 0.7275 0.2597 132 A 0.0203 0.6920 0.2877 133 E 0.0171 0.6843 0.2986 134 A 0.0253 0.6453 0.3295 135 A 0.0269 0.5867 0.3864 136 E 0.0247 0.5789 0.3964 137 S 0.0299 0.6139 0.3562 138 S 0.0275 0.6119 0.3607 139 A 0.0339 0.5335 0.4327 140 A 0.0343 0.3728 0.5930 141 E 0.0234 0.1118 0.8648