# This file is the result of combining several RDB files, specifically # T0245.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0245.t2k.stride-ebghtl.rdb (weight 1.24869) # T0245.t2k.str2.rdb (weight 1.54758) # T0245.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 T0245.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0245 # 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 T0245.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 33 # # ============================================ # Comments from T0245.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0245 # 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 T0245.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 33 # # ============================================ # Comments from T0245.t2k.str2.rdb # ============================================ # TARGET T0245 # 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 T0245.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 33 # # ============================================ # Comments from T0245.t2k.alpha.rdb # ============================================ # TARGET T0245 # 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 T0245.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 33 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0660 0.0625 0.8715 2 M 0.0808 0.1439 0.7753 3 W 0.0192 0.7263 0.2544 4 E 0.0093 0.8809 0.1099 5 Q 0.0065 0.9126 0.0809 6 F 0.0072 0.9184 0.0744 7 K 0.0061 0.9348 0.0592 8 K 0.0057 0.9374 0.0569 9 E 0.0058 0.9350 0.0592 10 K 0.0055 0.9244 0.0701 11 L 0.0061 0.9021 0.0918 12 R 0.0079 0.8205 0.1716 13 G 0.0116 0.6741 0.3143 14 Y 0.0331 0.6052 0.3618 15 L 0.0152 0.6312 0.3535 16 E 0.0201 0.5780 0.4019 17 A 0.0396 0.4997 0.4607 18 K 0.0546 0.3466 0.5989 19 N 0.0395 0.3349 0.6256 20 Q 0.0547 0.2013 0.7440 21 R 0.0572 0.1027 0.8401 22 K 0.1576 0.0520 0.7904 23 V 0.3241 0.0519 0.6240 24 D 0.1228 0.0516 0.8256 25 F 0.0106 0.6253 0.3640 26 D 0.0088 0.6522 0.3390 27 I 0.0094 0.8250 0.1656 28 V 0.0065 0.9088 0.0847 29 E 0.0068 0.9251 0.0681 30 L 0.0056 0.9427 0.0517 31 L 0.0053 0.9464 0.0483 32 D 0.0059 0.9374 0.0567 33 L 0.0056 0.9266 0.0678 34 I 0.0101 0.8816 0.1083 35 N 0.0266 0.6886 0.2848 36 S 0.0329 0.3425 0.6246 37 F 0.0666 0.1544 0.7790 38 D 0.0338 0.1512 0.8150 39 D 0.0502 0.0977 0.8521 40 F 0.4512 0.0603 0.4885 41 V 0.7294 0.0212 0.2494 42 T 0.7141 0.0243 0.2616 43 L 0.4812 0.0401 0.4786 44 S 0.2624 0.0708 0.6668 45 S 0.2133 0.1115 0.6752 46 C 0.2507 0.1198 0.6295 47 S 0.2217 0.0927 0.6856 48 G 0.3150 0.0419 0.6430 49 R 0.5932 0.0192 0.3876 50 I 0.8029 0.0105 0.1865 51 A 0.8924 0.0066 0.1010 52 V 0.9046 0.0061 0.0893 53 V 0.8900 0.0083 0.1017 54 D 0.8338 0.0139 0.1523 55 L 0.5813 0.0184 0.4003 56 E 0.3231 0.0496 0.6273 57 K 0.2120 0.0822 0.7059 58 P 0.1299 0.1320 0.7381 59 G 0.0909 0.1169 0.7922 60 D 0.0626 0.1397 0.7977 61 K 0.0905 0.1081 0.8014 62 A 0.1351 0.1078 0.7572 63 S 0.1970 0.0562 0.7468 64 S 0.5234 0.0232 0.4534 65 L 0.7589 0.0146 0.2265 66 F 0.8603 0.0132 0.1265 67 L 0.8445 0.0180 0.1375 68 G 0.8049 0.0208 0.1743 69 K 0.7106 0.0332 0.2562 70 W 0.5810 0.0339 0.3851 71 H 0.3242 0.0574 0.6184 72 E 0.2185 0.0479 0.7336 73 G 0.1899 0.0556 0.7545 74 V 0.1612 0.0450 0.7938 75 E 0.1103 0.0383 0.8514 76 V 0.0140 0.8341 0.1519 77 S 0.0067 0.9004 0.0928 78 E 0.0074 0.9224 0.0703 79 V 0.0081 0.9297 0.0622 80 A 0.0087 0.9311 0.0602 81 E 0.0101 0.9160 0.0739 82 A 0.0103 0.8983 0.0914 83 A 0.0262 0.8455 0.1283 84 L 0.0334 0.6944 0.2722 85 R 0.0327 0.4088 0.5584 86 S 0.0606 0.1169 0.8225 87 R 0.0768 0.0579 0.8653 88 K 0.0909 0.0522 0.8569 89 V 0.5612 0.0203 0.4185 90 A 0.8617 0.0062 0.1320 91 W 0.9072 0.0042 0.0886 92 L 0.8911 0.0051 0.1038 93 I 0.8410 0.0053 0.1536 94 Q 0.6224 0.0104 0.3672 95 Y 0.3387 0.0207 0.6406 96 P 0.2710 0.0175 0.7115 97 P 0.5200 0.0136 0.4664 98 I 0.7964 0.0071 0.1965 99 I 0.8787 0.0062 0.1151 100 H 0.9031 0.0049 0.0921 101 V 0.8915 0.0071 0.1014 102 A 0.8288 0.0092 0.1619 103 C 0.6316 0.0110 0.3574 104 R 0.2273 0.0477 0.7250 105 N 0.1602 0.0129 0.8269 106 I 0.0062 0.8688 0.1250 107 G 0.0049 0.9272 0.0679 108 A 0.0051 0.9419 0.0530 109 A 0.0047 0.9570 0.0383 110 K 0.0047 0.9584 0.0369 111 L 0.0047 0.9580 0.0373 112 L 0.0047 0.9586 0.0367 113 M 0.0047 0.9592 0.0361 114 N 0.0048 0.9582 0.0370 115 A 0.0047 0.9571 0.0382 116 A 0.0048 0.9535 0.0417 117 N 0.0050 0.9375 0.0575 118 T 0.0064 0.8881 0.1055 119 A 0.0421 0.5666 0.3914 120 G 0.0433 0.1562 0.8005 121 F 0.0880 0.1868 0.7251 122 R 0.1705 0.2684 0.5611 123 R 0.1979 0.2968 0.5053 124 S 0.1973 0.1920 0.6107 125 G 0.2723 0.0856 0.6420 126 V 0.5161 0.0616 0.4223 127 I 0.6171 0.0603 0.3226 128 S 0.4726 0.0520 0.4755 129 L 0.2753 0.0605 0.6641 130 S 0.1088 0.0663 0.8249 131 N 0.1579 0.0438 0.7983 132 Y 0.6454 0.0095 0.3451 133 V 0.8889 0.0038 0.1073 134 V 0.9197 0.0041 0.0762 135 E 0.9228 0.0038 0.0734 136 I 0.9078 0.0051 0.0871 137 A 0.8234 0.0101 0.1665 138 S 0.5843 0.0230 0.3928 139 L 0.3684 0.0466 0.5850 140 E 0.4255 0.0624 0.5122 141 R 0.5992 0.0367 0.3641 142 I 0.6965 0.0182 0.2853 143 E 0.7224 0.0214 0.2562 144 L 0.6838 0.0191 0.2971 145 P 0.6620 0.0189 0.3191 146 V 0.5542 0.0677 0.3781 147 A 0.4683 0.0734 0.4583 148 E 0.3216 0.0875 0.5909 149 K 0.1461 0.0697 0.7842 150 G 0.1744 0.0645 0.7611 151 L 0.5001 0.0401 0.4598 152 M 0.7208 0.0261 0.2531 153 L 0.7271 0.0209 0.2520 154 V 0.5414 0.0187 0.4400 155 D 0.1389 0.0232 0.8379 156 D 0.0052 0.9014 0.0934 157 A 0.0049 0.9319 0.0633 158 Y 0.0050 0.9456 0.0494 159 L 0.0047 0.9578 0.0375 160 S 0.0047 0.9592 0.0361 161 Y 0.0047 0.9595 0.0358 162 V 0.0047 0.9598 0.0355 163 V 0.0047 0.9603 0.0350 164 R 0.0047 0.9589 0.0364 165 W 0.0049 0.9544 0.0407 166 A 0.0049 0.9511 0.0440 167 N 0.0049 0.9496 0.0455 168 E 0.0051 0.9519 0.0430 169 K 0.0050 0.9501 0.0449 170 L 0.0051 0.9508 0.0441 171 L 0.0050 0.9477 0.0473 172 K 0.0074 0.9074 0.0852 173 G 0.0095 0.8273 0.1632 174 K 0.0054 0.8593 0.1353 175 E 0.0055 0.8922 0.1023 176 K 0.0052 0.9041 0.0908 177 L 0.0050 0.9412 0.0538 178 G 0.0048 0.9517 0.0435 179 R 0.0048 0.9522 0.0430 180 L 0.0047 0.9561 0.0391 181 Q 0.0047 0.9591 0.0362 182 E 0.0048 0.9560 0.0392 183 A 0.0048 0.9541 0.0411 184 L 0.0049 0.9510 0.0442 185 E 0.0051 0.9334 0.0615 186 S 0.0054 0.9056 0.0891 187 L 0.0071 0.8706 0.1223 188 Q 0.0102 0.8440 0.1458 189 R 0.0135 0.7971 0.1894 190 E 0.0280 0.6736 0.2984 191 N 0.0414 0.5471 0.4115 192 A 0.0587 0.4075 0.5338 193 Y 0.1054 0.3278 0.5667 194 C 0.1169 0.1973 0.6858 195 S 0.0730 0.1262 0.8008 196 D 0.0413 0.0460 0.9127