# This file is the result of combining several RDB files, specifically # T0161.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0161.t2k.stride-ebghtl.rdb (weight 1.24869) # T0161.t2k.str.rdb (weight 1.53983) # T0161.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 T0161.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0161 # 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 T0161.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 1 # # ============================================ # Comments from T0161.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0161 # 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 T0161.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 1 # # ============================================ # Comments from T0161.t2k.str.rdb # ============================================ # TARGET T0161 # 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 T0161.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 1 # # ============================================ # Comments from T0161.t2k.alpha.rdb # ============================================ # TARGET T0161 # 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 T0161.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0522 0.0670 0.8808 2 S 0.0726 0.1379 0.7894 3 E 0.0532 0.4911 0.4558 4 T 0.0414 0.5926 0.3660 5 D 0.0568 0.6558 0.2874 6 L 0.0832 0.7141 0.2027 7 L 0.1007 0.7404 0.1590 8 L 0.0980 0.7717 0.1303 9 K 0.0904 0.7499 0.1598 10 M 0.0946 0.6909 0.2145 11 V 0.1320 0.5799 0.2881 12 R 0.1166 0.4694 0.4140 13 Q 0.1255 0.2906 0.5839 14 P 0.1622 0.2599 0.5779 15 V 0.2784 0.2620 0.4596 16 K 0.3412 0.3036 0.3552 17 L 0.3159 0.4390 0.2451 18 Y 0.2678 0.4761 0.2562 19 S 0.2770 0.4623 0.2607 20 V 0.1487 0.6828 0.1685 21 A 0.1195 0.7234 0.1571 22 T 0.1104 0.7340 0.1556 23 L 0.0899 0.7413 0.1688 24 F 0.0664 0.7526 0.1810 25 H 0.0471 0.7682 0.1848 26 E 0.0399 0.7493 0.2108 27 F 0.0333 0.8099 0.1567 28 S 0.0242 0.8354 0.1405 29 E 0.0259 0.8437 0.1304 30 V 0.0353 0.8496 0.1151 31 I 0.0544 0.8170 0.1286 32 T 0.0585 0.7920 0.1495 33 K 0.0666 0.7418 0.1916 34 L 0.0797 0.6775 0.2428 35 E 0.0738 0.6299 0.2963 36 H 0.0733 0.5480 0.3787 37 S 0.0891 0.4772 0.4337 38 V 0.1177 0.4305 0.4518 39 Q 0.1283 0.3350 0.5368 40 K 0.1085 0.3161 0.5755 41 E 0.1098 0.1830 0.7071 42 P 0.0943 0.2282 0.6775 43 T 0.1123 0.3093 0.5784 44 S 0.1449 0.3541 0.5010 45 L 0.1685 0.3854 0.4461 46 L 0.1680 0.3260 0.5060 47 S 0.1243 0.2716 0.6041 48 E 0.0506 0.5172 0.4323 49 E 0.0316 0.5831 0.3853 50 N 0.0388 0.5673 0.3939 51 W 0.0306 0.6784 0.2910 52 H 0.0233 0.7707 0.2060 53 K 0.0159 0.8525 0.1316 54 Q 0.0172 0.8504 0.1325 55 F 0.0203 0.8636 0.1161 56 L 0.0253 0.8674 0.1073 57 K 0.0266 0.8506 0.1229 58 F 0.0224 0.8560 0.1216 59 A 0.0258 0.8194 0.1548 60 Q 0.0294 0.7382 0.2324 61 A 0.0443 0.6116 0.3440 62 L 0.0904 0.3184 0.5912 63 P 0.0764 0.2679 0.6557 64 A 0.0750 0.3106 0.6145 65 H 0.0794 0.2326 0.6880 66 G 0.0809 0.1615 0.7576 67 S 0.1105 0.2028 0.6867 68 A 0.1402 0.3395 0.5203 69 S 0.1344 0.3936 0.4720 70 W 0.1921 0.4080 0.3999 71 L 0.2035 0.3314 0.4651 72 N 0.2103 0.2033 0.5864 73 L 0.0657 0.4875 0.4468 74 D 0.0382 0.6178 0.3440 75 D 0.0231 0.7595 0.2173 76 A 0.0228 0.8268 0.1504 77 L 0.0321 0.8337 0.1341 78 Q 0.0359 0.8352 0.1289 79 A 0.0440 0.8098 0.1462 80 V 0.0560 0.7556 0.1884 81 V 0.0689 0.6134 0.3177 82 G 0.0522 0.4218 0.5260 83 N 0.0445 0.3471 0.6084 84 S 0.0453 0.4651 0.4896 85 R 0.0262 0.6752 0.2986 86 S 0.0217 0.7668 0.2115 87 A 0.0175 0.8409 0.1416 88 F 0.0222 0.8501 0.1277 89 L 0.0181 0.8943 0.0876 90 H 0.0185 0.9056 0.0760 91 Q 0.0184 0.9075 0.0741 92 L 0.0128 0.9193 0.0679 93 I 0.0118 0.9109 0.0773 94 A 0.0127 0.8860 0.1012 95 K 0.0144 0.8364 0.1493 96 L 0.0291 0.7448 0.2261 97 K 0.0335 0.6704 0.2960 98 S 0.0429 0.5933 0.3638 99 R 0.0594 0.5136 0.4270 100 H 0.1423 0.4246 0.4331 101 L 0.2716 0.3598 0.3686 102 Q 0.3637 0.3465 0.2898 103 V 0.4954 0.3049 0.1997 104 L 0.4999 0.2907 0.2094 105 E 0.4917 0.2593 0.2490 106 L 0.3395 0.3170 0.3435 107 N 0.2389 0.2727 0.4885 108 K 0.1859 0.2591 0.5550 109 I 0.1679 0.1721 0.6600 110 G 0.1229 0.0974 0.7796 111 S 0.1279 0.0901 0.7820 112 E 0.1387 0.0763 0.7849 113 P 0.1796 0.1094 0.7110 114 L 0.2037 0.1203 0.6760 115 D 0.1914 0.1269 0.6817 116 L 0.0892 0.3763 0.5345 117 S 0.0501 0.3451 0.6048 118 N 0.0652 0.2448 0.6900 119 L 0.1251 0.0757 0.7992 120 P 0.1368 0.0709 0.7923 121 A 0.1780 0.0865 0.7355 122 P 0.2470 0.1394 0.6136 123 F 0.4702 0.1629 0.3669 124 Y 0.6542 0.1305 0.2153 125 V 0.7030 0.1056 0.1914 126 L 0.6322 0.0962 0.2716 127 L 0.3539 0.0645 0.5816 128 P 0.1258 0.2466 0.6276 129 E 0.0375 0.5233 0.4392 130 S 0.0455 0.5676 0.3869 131 F 0.0590 0.6281 0.3129 132 A 0.0862 0.6583 0.2555 133 A 0.1248 0.6485 0.2266 134 R 0.1915 0.6070 0.2015 135 I 0.3015 0.5273 0.1712 136 T 0.3260 0.5279 0.1461 137 L 0.4087 0.4512 0.1401 138 L 0.4205 0.4134 0.1661 139 V 0.3661 0.3870 0.2469 140 Q 0.2279 0.3604 0.4117 141 D 0.1448 0.3184 0.5368 142 K 0.1114 0.2965 0.5921 143 A 0.1351 0.2474 0.6174 144 L 0.1801 0.1444 0.6755 145 P 0.2246 0.1726 0.6029 146 Y 0.4859 0.1477 0.3663 147 V 0.6666 0.1136 0.2197 148 R 0.7452 0.0807 0.1741 149 V 0.7182 0.0927 0.1890 150 S 0.6477 0.1132 0.2391 151 F 0.5597 0.2016 0.2387 152 E 0.4888 0.2298 0.2815 153 Y 0.4435 0.2171 0.3394 154 W 0.3408 0.1840 0.4752 155 H 0.1649 0.1167 0.7184 156 A 0.0406 0.0415 0.9179