# This file is the result of combining several RDB files, specifically # T0346.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0346.t2k.stride-ebghtl.rdb (weight 1.24869) # T0346.t2k.str2.rdb (weight 1.54758) # T0346.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 T0346.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0346 # 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 T0346.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 1396 # # ============================================ # Comments from T0346.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0346 # 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 T0346.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 1396 # # ============================================ # Comments from T0346.t2k.str2.rdb # ============================================ # TARGET T0346 # 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 T0346.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 1396 # # ============================================ # Comments from T0346.t2k.alpha.rdb # ============================================ # TARGET T0346 # 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 T0346.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 1396 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1246 0.0229 0.8524 2 P 0.2276 0.0289 0.7435 3 Q 0.6372 0.0253 0.3375 4 C 0.8496 0.0159 0.1345 5 H 0.8726 0.0161 0.1112 6 F 0.8463 0.0125 0.1412 7 D 0.7607 0.0247 0.2146 8 I 0.7454 0.0340 0.2206 9 E 0.7461 0.0369 0.2170 10 I 0.6712 0.0504 0.2785 11 N 0.4843 0.0457 0.4700 12 R 0.3360 0.0464 0.6176 13 E 0.4035 0.0202 0.5763 14 P 0.4660 0.0325 0.5015 15 V 0.4307 0.0472 0.5221 16 G 0.5530 0.0244 0.4226 17 R 0.7674 0.0075 0.2251 18 I 0.8850 0.0039 0.1111 19 M 0.9159 0.0045 0.0796 20 F 0.9175 0.0045 0.0780 21 Q 0.8982 0.0054 0.0964 22 L 0.7622 0.0130 0.2248 23 F 0.4123 0.0329 0.5548 24 S 0.0721 0.3210 0.6070 25 D 0.0300 0.3568 0.6132 26 I 0.0603 0.3049 0.6348 27 C 0.0696 0.1820 0.7483 28 P 0.0379 0.6715 0.2907 29 K 0.0220 0.8274 0.1506 30 T 0.0125 0.8995 0.0880 31 C 0.0061 0.9468 0.0471 32 K 0.0052 0.9541 0.0407 33 N 0.0055 0.9506 0.0440 34 F 0.0048 0.9532 0.0420 35 L 0.0053 0.9526 0.0421 36 C 0.0058 0.9479 0.0464 37 L 0.0073 0.9279 0.0647 38 C 0.0219 0.8487 0.1294 39 S 0.0294 0.6822 0.2885 40 G 0.0477 0.3307 0.6216 41 E 0.0556 0.2079 0.7365 42 K 0.0893 0.2566 0.6541 43 G 0.0938 0.2712 0.6350 44 L 0.1266 0.2282 0.6452 45 G 0.1817 0.1678 0.6505 46 K 0.1415 0.1597 0.6988 47 T 0.1113 0.1719 0.7168 48 T 0.1047 0.1135 0.7818 49 G 0.1278 0.0832 0.7891 50 K 0.2392 0.0654 0.6953 51 K 0.3272 0.0804 0.5923 52 L 0.3845 0.0904 0.5251 53 C 0.3912 0.0789 0.5299 54 Y 0.3572 0.0674 0.5753 55 K 0.1509 0.0834 0.7657 56 G 0.1290 0.0534 0.8176 57 S 0.3432 0.0367 0.6201 58 T 0.5747 0.0540 0.3713 59 F 0.6511 0.0806 0.2683 60 H 0.6977 0.0777 0.2246 61 R 0.7309 0.0751 0.1940 62 V 0.6946 0.0687 0.2367 63 V 0.4448 0.0479 0.5073 64 K 0.0703 0.1067 0.8230 65 N 0.0520 0.0714 0.8765 66 F 0.4764 0.0584 0.4652 67 M 0.7889 0.0218 0.1893 68 I 0.8273 0.0136 0.1592 69 Q 0.7321 0.0267 0.2412 70 G 0.5162 0.0336 0.4503 71 G 0.3571 0.0371 0.6058 72 D 0.2358 0.0399 0.7243 73 F 0.1426 0.0942 0.7632 74 S 0.1045 0.0862 0.8093 75 E 0.0915 0.0758 0.8328 76 G 0.0930 0.0738 0.8332 77 N 0.1196 0.0883 0.7920 78 G 0.1130 0.0817 0.8053 79 K 0.1344 0.0837 0.7819 80 G 0.1216 0.0882 0.7901 81 G 0.1497 0.1364 0.7139 82 E 0.2739 0.1532 0.5729 83 S 0.3223 0.1567 0.5210 84 I 0.2975 0.1786 0.5239 85 Y 0.1977 0.1550 0.6473 86 G 0.1407 0.1237 0.7357 87 G 0.1468 0.1319 0.7213 88 Y 0.1844 0.1393 0.6763 89 F 0.1420 0.1616 0.6963 90 K 0.0963 0.2463 0.6574 91 D 0.0654 0.3938 0.5408 92 E 0.0741 0.3778 0.5481 93 N 0.1009 0.2777 0.6215 94 F 0.0949 0.2640 0.6411 95 I 0.1184 0.2443 0.6374 96 L 0.1461 0.2677 0.5862 97 K 0.1210 0.2311 0.6479 98 H 0.1276 0.1546 0.7179 99 D 0.1108 0.1012 0.7879 100 R 0.1186 0.1332 0.7482 101 A 0.1662 0.2558 0.5780 102 F 0.4142 0.2057 0.3800 103 L 0.6175 0.2022 0.1804 104 L 0.6847 0.1786 0.1367 105 S 0.5968 0.2361 0.1670 106 M 0.4971 0.2902 0.2127 107 A 0.3568 0.3027 0.3405 108 N 0.2405 0.1990 0.5605 109 R 0.1746 0.0780 0.7474 110 G 0.0958 0.0339 0.8703 111 K 0.0760 0.0912 0.8328 112 H 0.0717 0.0799 0.8484 113 T 0.0806 0.0993 0.8201 114 N 0.1090 0.0795 0.8115 115 G 0.1272 0.0824 0.7904 116 S 0.3531 0.0277 0.6192 117 Q 0.7270 0.0180 0.2550 118 F 0.8722 0.0075 0.1202 119 F 0.8912 0.0080 0.1008 120 I 0.8887 0.0074 0.1039 121 T 0.8330 0.0091 0.1579 122 T 0.6056 0.0274 0.3670 123 K 0.2880 0.0246 0.6874 124 P 0.1692 0.0479 0.7829 125 A 0.1538 0.0609 0.7853 126 P 0.1070 0.2470 0.6461 127 H 0.1394 0.2568 0.6038 128 L 0.1336 0.1892 0.6772 129 D 0.0883 0.0702 0.8415 130 G 0.0512 0.0742 0.8745 131 V 0.1941 0.0499 0.7560 132 H 0.6965 0.0156 0.2879 133 V 0.8604 0.0073 0.1322 134 V 0.8999 0.0059 0.0942 135 F 0.8395 0.0213 0.1391 136 G 0.7972 0.0196 0.1831 137 L 0.8232 0.0190 0.1578 138 V 0.7489 0.0496 0.2015 139 I 0.5443 0.0960 0.3596 140 S 0.2035 0.1396 0.6569 141 G 0.0863 0.1999 0.7138 142 F 0.0669 0.6578 0.2753 143 E 0.0579 0.8097 0.1324 144 V 0.0123 0.9221 0.0657 145 I 0.0084 0.9443 0.0472 146 E 0.0111 0.9396 0.0492 147 Q 0.0092 0.9340 0.0568 148 I 0.0122 0.9150 0.0728 149 E 0.0187 0.8092 0.1721 150 N 0.0286 0.5982 0.3732 151 L 0.1106 0.1657 0.7238 152 K 0.1585 0.0604 0.7810 153 T 0.1934 0.0459 0.7607 154 D 0.0866 0.0607 0.8527 155 A 0.0274 0.1125 0.8601 156 A 0.0467 0.0524 0.9010 157 S 0.0522 0.0388 0.9091 158 R 0.1696 0.0134 0.8170 159 P 0.3716 0.0108 0.6176 160 Y 0.3362 0.0287 0.6351 161 A 0.4073 0.0229 0.5698 162 D 0.4948 0.0156 0.4897 163 V 0.7340 0.0052 0.2609 164 R 0.8759 0.0043 0.1198 165 V 0.8858 0.0034 0.1108 166 I 0.7847 0.0197 0.1956 167 D 0.6596 0.0132 0.3273 168 C 0.4515 0.0533 0.4952 169 G 0.5397 0.0370 0.4234 170 V 0.5558 0.0325 0.4116 171 L 0.2564 0.0327 0.7109 172 A 0.0696 0.0177 0.9127