# This file is the result of combining several RDB files, specifically # T0132.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0132.t2k.stride-ebghtl.rdb (weight 1.24869) # T0132.t2k.str.rdb (weight 1.53983) # 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 T0132.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0132 # 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 T0132.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 94 # # ============================================ # Comments from T0132.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0132 # 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 T0132.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 94 # # ============================================ # Comments from T0132.t2k.str.rdb # ============================================ # TARGET T0132 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0132.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 94 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0265 0.0195 0.9540 2 S 0.1009 0.0595 0.8395 3 A 0.1379 0.0767 0.7854 4 N 0.1504 0.0682 0.7814 5 F 0.1324 0.0339 0.8336 6 T 0.0959 0.0284 0.8757 7 D 0.0944 0.1224 0.7832 8 K 0.1246 0.1300 0.7455 9 N 0.2945 0.1166 0.5890 10 G 0.3992 0.0482 0.5526 11 R 0.3840 0.0337 0.5823 12 Q 0.2040 0.0437 0.7523 13 S 0.1295 0.0506 0.8199 14 K 0.0694 0.0717 0.8589 15 G 0.1916 0.0471 0.7613 16 V 0.6778 0.0153 0.3069 17 L 0.9042 0.0048 0.0910 18 L 0.9381 0.0042 0.0577 19 L 0.9424 0.0049 0.0527 20 R 0.9265 0.0064 0.0671 21 T 0.9004 0.0072 0.0924 22 L 0.8564 0.0062 0.1374 23 A 0.7325 0.0077 0.2598 24 M 0.3961 0.0136 0.5902 25 P 0.1179 0.2346 0.6475 26 S 0.0456 0.3543 0.6001 27 D 0.0588 0.4140 0.5272 28 T 0.1249 0.1611 0.7140 29 N 0.0666 0.1061 0.8274 30 A 0.0382 0.2032 0.7586 31 N 0.0287 0.2096 0.7617 32 G 0.0720 0.2245 0.7035 33 D 0.2479 0.3462 0.4059 34 I 0.3549 0.4155 0.2296 35 F 0.2009 0.5459 0.2532 36 G 0.0736 0.7492 0.1773 37 G 0.0263 0.8330 0.1408 38 W 0.0075 0.9604 0.0322 39 I 0.0057 0.9649 0.0295 40 M 0.0044 0.9607 0.0349 41 S 0.0044 0.9564 0.0392 42 Q 0.0038 0.9582 0.0381 43 M 0.0037 0.9627 0.0336 44 D 0.0038 0.9670 0.0292 45 M 0.0037 0.9727 0.0236 46 G 0.0037 0.9752 0.0211 47 G 0.0037 0.9759 0.0204 48 A 0.0037 0.9766 0.0197 49 I 0.0037 0.9766 0.0197 50 L 0.0037 0.9748 0.0215 51 A 0.0037 0.9739 0.0224 52 K 0.0037 0.9644 0.0319 53 E 0.0044 0.9283 0.0672 54 I 0.0089 0.8087 0.1824 55 A 0.0228 0.3469 0.6304 56 H 0.0166 0.0904 0.8930 57 G 0.0439 0.0399 0.9162 58 R 0.1934 0.0214 0.7852 59 V 0.6233 0.0076 0.3691 60 V 0.9056 0.0061 0.0883 61 T 0.9571 0.0046 0.0384 62 V 0.9486 0.0061 0.0453 63 A 0.9152 0.0073 0.0775 64 V 0.7747 0.0357 0.1896 65 E 0.4198 0.0839 0.4963 66 S 0.4637 0.0903 0.4460 67 M 0.8234 0.0086 0.1680 68 N 0.8700 0.0046 0.1254 69 F 0.8660 0.0084 0.1256 70 I 0.7934 0.0085 0.1982 71 K 0.5922 0.0055 0.4023 72 P 0.5633 0.0048 0.4319 73 I 0.6039 0.0038 0.3923 74 S 0.3995 0.0102 0.5902 75 V 0.1469 0.0395 0.8137 76 G 0.0364 0.0305 0.9332 77 D 0.2606 0.0230 0.7164 78 V 0.8475 0.0026 0.1500 79 V 0.9660 0.0024 0.0316 80 C 0.9773 0.0024 0.0203 81 C 0.9734 0.0024 0.0242 82 Y 0.9742 0.0024 0.0234 83 G 0.9734 0.0024 0.0241 84 Q 0.9755 0.0024 0.0221 85 C 0.9643 0.0025 0.0332 86 L 0.9360 0.0027 0.0612 87 K 0.8667 0.0048 0.1285 88 V 0.5292 0.0156 0.4552 89 G 0.2468 0.0174 0.7358 90 R 0.2768 0.0142 0.7091 91 S 0.5686 0.0069 0.4245 92 S 0.8474 0.0030 0.1496 93 I 0.9571 0.0025 0.0404 94 K 0.9741 0.0024 0.0234 95 I 0.9674 0.0024 0.0302 96 K 0.9758 0.0024 0.0218 97 V 0.9778 0.0024 0.0198 98 E 0.9772 0.0024 0.0204 99 V 0.9684 0.0025 0.0291 100 W 0.9532 0.0027 0.0441 101 V 0.8682 0.0057 0.1261 102 K 0.6217 0.0185 0.3598 103 K 0.3957 0.0329 0.5714 104 V 0.2555 0.0973 0.6471 105 A 0.1699 0.1143 0.7158 106 S 0.1375 0.0891 0.7734 107 E 0.0528 0.1058 0.8415 108 P 0.0661 0.0960 0.8379 109 I 0.1138 0.0963 0.7899 110 G 0.1680 0.0686 0.7633 111 E 0.3924 0.0824 0.5252 112 R 0.6226 0.0665 0.3110 113 Y 0.7590 0.0338 0.2071 114 C 0.8358 0.0229 0.1413 115 V 0.8605 0.0147 0.1248 116 T 0.8868 0.0093 0.1039 117 D 0.9146 0.0064 0.0790 118 A 0.9383 0.0039 0.0577 119 V 0.9656 0.0025 0.0319 120 F 0.9766 0.0024 0.0210 121 T 0.9765 0.0024 0.0211 122 F 0.9692 0.0024 0.0284 123 V 0.9524 0.0026 0.0450 124 A 0.8986 0.0030 0.0984 125 V 0.8176 0.0035 0.1789 126 D 0.2220 0.0123 0.7657 127 N 0.0162 0.0266 0.9572 128 N 0.0084 0.0208 0.9708 129 G 0.0393 0.0202 0.9405 130 R 0.1381 0.0057 0.8562 131 S 0.5846 0.0047 0.4107 132 R 0.3827 0.0074 0.6099 133 T 0.3001 0.0109 0.6889 134 I 0.1725 0.0153 0.8122 135 P 0.1155 0.0235 0.8610 136 R 0.0955 0.0280 0.8765 137 E 0.1046 0.0390 0.8564 138 N 0.1908 0.0381 0.7710 139 N 0.1602 0.0224 0.8174 140 Q 0.1162 0.0223 0.8615 141 E 0.0469 0.0174 0.9357 142 L 0.0201 0.0488 0.9310 143 E 0.0040 0.9248 0.0711 144 K 0.0039 0.9377 0.0584 145 A 0.0038 0.9567 0.0395 146 L 0.0042 0.9577 0.0381 147 A 0.0046 0.9455 0.0499 148 L 0.0041 0.9328 0.0631 149 I 0.0052 0.9014 0.0934 150 S 0.0054 0.8860 0.1087 151 E 0.0056 0.8020 0.1925 152 Q 0.0097 0.6393 0.3509 153 P 0.0177 0.4486 0.5336 154 L 0.0095 0.0340 0.9565