# This file is the result of combining several RDB files, specifically # T0240.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0240.t2k.stride-ebghtl.rdb (weight 1.24869) # T0240.t2k.str2.rdb (weight 1.54758) # T0240.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 T0240.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0240 # 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 T0240.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 138 # # ============================================ # Comments from T0240.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0240 # 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 T0240.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 138 # # ============================================ # Comments from T0240.t2k.str2.rdb # ============================================ # TARGET T0240 # 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 T0240.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 138 # # ============================================ # Comments from T0240.t2k.alpha.rdb # ============================================ # TARGET T0240 # 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 T0240.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 138 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0441 0.1291 0.8268 2 S 0.0800 0.1220 0.7980 3 G 0.0707 0.1314 0.7980 4 P 0.1175 0.1823 0.7002 5 R 0.1620 0.1977 0.6403 6 A 0.1954 0.2045 0.6001 7 L 0.1746 0.2295 0.5959 8 S 0.1372 0.1917 0.6711 9 R 0.1131 0.0915 0.7954 10 N 0.0911 0.0497 0.8592 11 Q 0.0732 0.0358 0.8909 12 P 0.0682 0.0817 0.8500 13 Q 0.0786 0.1368 0.7846 14 Y 0.0642 0.0994 0.8363 15 P 0.0292 0.4097 0.5611 16 A 0.0059 0.9162 0.0779 17 R 0.0055 0.9443 0.0502 18 A 0.0053 0.9466 0.0482 19 Q 0.0064 0.9280 0.0656 20 A 0.0089 0.8396 0.1516 21 L 0.0422 0.3027 0.6550 22 R 0.0331 0.0416 0.9253 23 I 0.0870 0.0367 0.8763 24 E 0.3367 0.0319 0.6314 25 G 0.5335 0.0225 0.4440 26 Q 0.8222 0.0061 0.1717 27 V 0.9130 0.0034 0.0835 28 K 0.9290 0.0031 0.0679 29 V 0.9295 0.0031 0.0673 30 K 0.9281 0.0031 0.0688 31 F 0.9239 0.0035 0.0727 32 D 0.9004 0.0035 0.0961 33 V 0.8483 0.0058 0.1459 34 T 0.2474 0.0138 0.7388 35 P 0.0146 0.1138 0.8716 36 D 0.0489 0.0184 0.9327 37 G 0.0745 0.0275 0.8980 38 R 0.3422 0.0090 0.6488 39 V 0.8301 0.0036 0.1663 40 D 0.7703 0.0228 0.2069 41 N 0.8304 0.0066 0.1630 42 V 0.8491 0.0040 0.1469 43 Q 0.9038 0.0046 0.0916 44 I 0.9193 0.0033 0.0775 45 L 0.8358 0.0192 0.1451 46 S 0.6854 0.0204 0.2941 47 A 0.2965 0.0711 0.6324 48 K 0.1269 0.0604 0.8126 49 P 0.0741 0.0929 0.8330 50 A 0.0808 0.1842 0.7350 51 N 0.0262 0.5980 0.3757 52 M 0.0234 0.7193 0.2573 53 F 0.0226 0.7092 0.2682 54 E 0.0190 0.7882 0.1928 55 R 0.0051 0.9524 0.0425 56 E 0.0051 0.9575 0.0375 57 V 0.0048 0.9579 0.0374 58 K 0.0047 0.9595 0.0358 59 N 0.0048 0.9586 0.0366 60 A 0.0048 0.9554 0.0399 61 M 0.0052 0.9421 0.0527 62 R 0.0061 0.9022 0.0917 63 R 0.0130 0.6596 0.3274 64 W 0.0624 0.2820 0.6556 65 R 0.0982 0.1144 0.7874 66 Y 0.2613 0.0650 0.6737 67 E 0.2816 0.0287 0.6896 68 P 0.2856 0.0370 0.6774 69 G 0.3123 0.0507 0.6369 70 K 0.1870 0.0684 0.7445 71 P 0.1085 0.1064 0.7851 72 G 0.0642 0.0564 0.8794 73 S 0.0637 0.0461 0.8902 74 G 0.2816 0.0211 0.6973 75 I 0.5645 0.0148 0.4207 76 V 0.6018 0.0216 0.3766 77 V 0.6270 0.0274 0.3456 78 N 0.5735 0.0268 0.3998 79 I 0.6544 0.0172 0.3284 80 L 0.7464 0.0119 0.2417 81 F 0.7924 0.0082 0.1994 82 K 0.7981 0.0131 0.1888 83 I 0.7285 0.0131 0.2584 84 N 0.6981 0.0205 0.2814 85 G 0.6830 0.0256 0.2914 86 T 0.6310 0.0312 0.3378 87 T 0.4674 0.0404 0.4922 88 E 0.2787 0.0940 0.6272 89 I 0.1340 0.1045 0.7615 90 Q 0.0859 0.1189 0.7952 91 A 0.0503 0.2071 0.7426 92 S 0.0481 0.2054 0.7465 93 G 0.0535 0.2538 0.6927 94 P 0.0464 0.5542 0.3994 95 R 0.0290 0.7144 0.2567 96 A 0.0227 0.7546 0.2228 97 L 0.0235 0.7076 0.2690 98 S 0.0319 0.6139 0.3542 99 R 0.0284 0.4642 0.5074 100 N 0.0320 0.3168 0.6511 101 Q 0.0759 0.1118 0.8123 102 P 0.0249 0.3552 0.6199 103 Q 0.0272 0.3718 0.6010 104 Y 0.0398 0.3731 0.5872 105 P 0.0285 0.6715 0.3001 106 A 0.0169 0.7946 0.1885 107 R 0.0084 0.8950 0.0967 108 A 0.0112 0.9139 0.0749 109 Q 0.0089 0.9236 0.0675 110 A 0.0094 0.9277 0.0629 111 L 0.0112 0.9010 0.0878 112 R 0.0119 0.8721 0.1161 113 I 0.0128 0.7627 0.2245 114 E 0.0511 0.2771 0.6718 115 G 0.0488 0.0506 0.9005 116 Q 0.1898 0.0179 0.7923 117 V 0.7020 0.0082 0.2898 118 K 0.8619 0.0054 0.1328 119 V 0.9019 0.0035 0.0945 120 K 0.8951 0.0041 0.1008 121 F 0.8763 0.0037 0.1201 122 D 0.8062 0.0039 0.1899 123 V 0.6828 0.0073 0.3098 124 T 0.1489 0.0152 0.8359 125 P 0.0159 0.1110 0.8731 126 D 0.0517 0.0256 0.9227 127 G 0.0742 0.0361 0.8897 128 R 0.2934 0.0249 0.6817 129 V 0.6851 0.0157 0.2993 130 D 0.5610 0.0363 0.4027 131 N 0.5345 0.0334 0.4321 132 V 0.7098 0.0129 0.2772 133 Q 0.8738 0.0056 0.1206 134 I 0.9124 0.0034 0.0842 135 L 0.8418 0.0110 0.1472 136 S 0.7792 0.0122 0.2086 137 A 0.6403 0.0228 0.3369 138 K 0.3477 0.0187 0.6335 139 P 0.1840 0.0205 0.7955 140 A 0.0620 0.1523 0.7858 141 N 0.0503 0.1665 0.7833 142 M 0.0301 0.3317 0.6382 143 F 0.0335 0.4578 0.5087 144 E 0.0061 0.8988 0.0951 145 R 0.0066 0.9218 0.0716 146 E 0.0067 0.9296 0.0637 147 V 0.0082 0.9369 0.0549 148 K 0.0071 0.9415 0.0514 149 N 0.0088 0.9225 0.0688 150 A 0.0121 0.8596 0.1283 151 M 0.0179 0.5402 0.4420 152 R 0.0280 0.2902 0.6819 153 R 0.0622 0.0904 0.8473 154 W 0.1306 0.0779 0.7915 155 R 0.2260 0.1131 0.6610 156 Y 0.2810 0.1070 0.6120 157 E 0.2148 0.0728 0.7124 158 P 0.0988 0.0896 0.8116 159 G 0.0719 0.0596 0.8685 160 K 0.1176 0.0412 0.8412 161 P 0.2128 0.0445 0.7427 162 G 0.2368 0.0485 0.7147 163 S 0.5103 0.0149 0.4748 164 G 0.7995 0.0083 0.1922 165 I 0.8694 0.0041 0.1265 166 V 0.8853 0.0041 0.1106 167 V 0.8625 0.0050 0.1326 168 N 0.8444 0.0041 0.1515 169 I 0.8871 0.0034 0.1095 170 L 0.9110 0.0045 0.0846 171 F 0.9076 0.0046 0.0878 172 K 0.8710 0.0059 0.1232 173 I 0.7159 0.0158 0.2684 174 N 0.2497 0.0366 0.7137 175 G 0.1352 0.0519 0.8129 176 T 0.2525 0.0902 0.6573 177 T 0.4688 0.0859 0.4454 178 E 0.5243 0.0750 0.4007 179 I 0.3534 0.0683 0.5783 180 Q 0.0718 0.0293 0.8989