# This file is the result of combining several RDB files, specifically # T0356.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0356.t2k.stride-ebghtl.rdb (weight 1.24869) # T0356.t2k.str2.rdb (weight 1.54758) # T0356.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 T0356.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 239 # # ============================================ # Comments from T0356.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 239 # # ============================================ # Comments from T0356.t2k.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 239 # # ============================================ # Comments from T0356.t2k.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 239 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0613 0.0612 0.8775 2 D 0.0823 0.1153 0.8024 3 A 0.0696 0.2094 0.7209 4 M 0.0667 0.2098 0.7235 5 K 0.0809 0.1928 0.7263 6 Y 0.0581 0.2819 0.6600 7 N 0.0406 0.3422 0.6172 8 D 0.0567 0.3348 0.6085 9 L 0.0056 0.9267 0.0676 10 R 0.0048 0.9559 0.0393 11 D 0.0048 0.9582 0.0370 12 F 0.0047 0.9588 0.0365 13 L 0.0047 0.9590 0.0363 14 T 0.0047 0.9574 0.0380 15 L 0.0047 0.9557 0.0396 16 L 0.0049 0.9553 0.0398 17 E 0.0057 0.9305 0.0638 18 Q 0.0069 0.8118 0.1814 19 Q 0.0464 0.1489 0.8047 20 G 0.0311 0.0221 0.9468 21 E 0.1356 0.0260 0.8383 22 L 0.6778 0.0080 0.3142 23 K 0.7954 0.0107 0.1940 24 R 0.8725 0.0057 0.1218 25 I 0.7907 0.0090 0.2003 26 T 0.4855 0.0179 0.4966 27 L 0.3562 0.0241 0.6197 28 P 0.2506 0.0241 0.7253 29 V 0.2409 0.0255 0.7336 30 D 0.1333 0.0233 0.8434 31 P 0.0165 0.5719 0.4116 32 H 0.0136 0.6926 0.2938 33 L 0.0123 0.8197 0.1680 34 E 0.0111 0.8911 0.0978 35 I 0.0048 0.9412 0.0540 36 T 0.0047 0.9534 0.0419 37 E 0.0047 0.9590 0.0364 38 I 0.0047 0.9598 0.0356 39 A 0.0047 0.9585 0.0368 40 D 0.0047 0.9581 0.0372 41 R 0.0048 0.9572 0.0380 42 T 0.0050 0.9522 0.0427 43 L 0.0060 0.9272 0.0668 44 R 0.0099 0.8490 0.1411 45 A 0.0416 0.4203 0.5381 46 G 0.0387 0.0407 0.9206 47 G 0.0629 0.0185 0.9187 48 P 0.1692 0.0233 0.8074 49 A 0.3774 0.0356 0.5870 50 L 0.5831 0.0487 0.3682 51 L 0.7078 0.0376 0.2547 52 F 0.6427 0.0366 0.3207 53 E 0.4816 0.0721 0.4463 54 N 0.2284 0.0424 0.7292 55 P 0.1044 0.0805 0.8151 56 K 0.0477 0.0971 0.8552 57 G 0.0446 0.0789 0.8765 58 Y 0.1116 0.0599 0.8285 59 S 0.1230 0.0743 0.8027 60 M 0.2186 0.0538 0.7276 61 P 0.3861 0.1099 0.5039 62 V 0.6535 0.1462 0.2003 63 L 0.6941 0.1432 0.1627 64 C 0.5458 0.2158 0.2384 65 N 0.3740 0.2095 0.4165 66 L 0.2041 0.2661 0.5298 67 F 0.1227 0.1982 0.6791 68 G 0.1000 0.1079 0.7921 69 T 0.0819 0.1477 0.7704 70 P 0.0053 0.9353 0.0593 71 K 0.0053 0.9477 0.0470 72 R 0.0051 0.9508 0.0440 73 V 0.0048 0.9553 0.0399 74 A 0.0050 0.9523 0.0428 75 M 0.0056 0.9364 0.0580 76 G 0.0084 0.8816 0.1100 77 M 0.0445 0.5153 0.4401 78 G 0.0400 0.0857 0.8743 79 Q 0.0579 0.0517 0.8904 80 E 0.0664 0.0776 0.8561 81 D 0.0337 0.4555 0.5108 82 V 0.0116 0.6144 0.3740 83 S 0.0151 0.6606 0.3243 84 A 0.0111 0.7879 0.2010 85 L 0.0064 0.8981 0.0955 86 R 0.0055 0.9273 0.0673 87 E 0.0054 0.9384 0.0562 88 V 0.0048 0.9476 0.0475 89 G 0.0050 0.9450 0.0501 90 K 0.0052 0.9362 0.0586 91 L 0.0052 0.9259 0.0690 92 L 0.0074 0.8890 0.1036 93 A 0.0088 0.7684 0.2228 94 F 0.0180 0.5862 0.3957 95 L 0.0334 0.4057 0.5609 96 K 0.0418 0.3246 0.6336 97 E 0.0494 0.1849 0.7657 98 P 0.0569 0.1180 0.8251 99 E 0.0745 0.0904 0.8350 100 P 0.0706 0.0840 0.8453 101 P 0.0582 0.2198 0.7220 102 K 0.0397 0.3085 0.6519 103 G 0.0588 0.2868 0.6544 104 F 0.0195 0.7245 0.2560 105 R 0.0090 0.8324 0.1586 106 D 0.0091 0.8534 0.1374 107 L 0.0058 0.8994 0.0948 108 F 0.0066 0.8883 0.1052 109 D 0.0075 0.7996 0.1929 110 K 0.0096 0.7437 0.2466 111 L 0.0297 0.6807 0.2896 112 P 0.0097 0.7759 0.2145 113 Q 0.0099 0.7820 0.2080 114 F 0.0093 0.8070 0.1836 115 K 0.0110 0.7472 0.2419 116 Q 0.0183 0.6314 0.3503 117 V 0.0351 0.5096 0.4552 118 L 0.0636 0.2616 0.6747 119 N 0.0668 0.1140 0.8193 120 M 0.0895 0.0504 0.8601 121 P 0.0885 0.0243 0.8873 122 T 0.1971 0.0301 0.7728 123 K 0.4615 0.0424 0.4961 124 R 0.4521 0.0400 0.5079 125 L 0.2841 0.0540 0.6619 126 R 0.1105 0.0797 0.8098 127 G 0.0807 0.0580 0.8613 128 A 0.0893 0.0340 0.8766 129 P 0.1453 0.1186 0.7361 130 C 0.3300 0.1839 0.4860 131 Q 0.4349 0.2370 0.3281 132 Q 0.5658 0.2092 0.2251 133 K 0.6117 0.1980 0.1904 134 I 0.6055 0.1910 0.2036 135 V 0.5159 0.1803 0.3038 136 S 0.2517 0.1752 0.5731 137 G 0.0998 0.1009 0.7993 138 D 0.0949 0.0951 0.8100 139 D 0.2109 0.0834 0.7058 140 V 0.2322 0.0726 0.6951 141 D 0.2163 0.0827 0.7010 142 L 0.0311 0.6901 0.2788 143 N 0.0211 0.6379 0.3409 144 R 0.0404 0.5490 0.4106 145 I 0.1400 0.0536 0.8064 146 P 0.1512 0.0450 0.8037 147 I 0.3561 0.0768 0.5670 148 M 0.3198 0.1304 0.5497 149 T 0.3658 0.1100 0.5242 150 C 0.3049 0.0800 0.6151 151 W 0.1200 0.0351 0.8450 152 P 0.0331 0.1672 0.7997 153 E 0.0323 0.1307 0.8369 154 D 0.0953 0.1324 0.7723 155 A 0.1142 0.1084 0.7774 156 A 0.1424 0.1038 0.7538 157 P 0.2225 0.1354 0.6421 158 L 0.5325 0.0958 0.3718 159 I 0.6966 0.0541 0.2493 160 T 0.6277 0.0366 0.3357 161 W 0.5225 0.0636 0.4139 162 G 0.5588 0.0640 0.3772 163 L 0.7774 0.0260 0.1966 164 T 0.8798 0.0126 0.1076 165 V 0.8905 0.0101 0.0994 166 T 0.8292 0.0177 0.1531 167 R 0.7147 0.0148 0.2704 168 G 0.2810 0.0164 0.7026 169 P 0.0183 0.1501 0.8315 170 H 0.0236 0.0995 0.8769 171 K 0.0808 0.0473 0.8719 172 E 0.1109 0.0366 0.8524 173 R 0.5309 0.0248 0.4444 174 Q 0.6984 0.0261 0.2756 175 N 0.7060 0.0327 0.2612 176 L 0.6766 0.0375 0.2858 177 G 0.6513 0.0412 0.3075 178 I 0.6201 0.0385 0.3414 179 Y 0.3519 0.0283 0.6198 180 R 0.0619 0.0301 0.9080