# This file is the result of combining several RDB files, specifically # T0557.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0557.t2k.stride-ebghtl.rdb (weight 1.24869) # T0557.t2k.str2.rdb (weight 1.54758) # T0557.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 T0557.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0557 # 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 T0557.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 164 # # ============================================ # Comments from T0557.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0557 # 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 T0557.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 164 # # ============================================ # Comments from T0557.t2k.str2.rdb # ============================================ # TARGET T0557 # 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 T0557.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 164 # # ============================================ # Comments from T0557.t2k.alpha.rdb # ============================================ # TARGET T0557 # 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 T0557.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 164 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0558 0.0884 0.8559 2 R 0.0890 0.2398 0.6713 3 S 0.0613 0.5865 0.3522 4 A 0.0132 0.8767 0.1101 5 T 0.0090 0.9213 0.0698 6 D 0.0067 0.9375 0.0558 7 L 0.0058 0.9457 0.0484 8 L 0.0060 0.9475 0.0465 9 D 0.0059 0.9474 0.0468 10 E 0.0051 0.9445 0.0504 11 L 0.0055 0.9291 0.0654 12 N 0.0078 0.8765 0.1158 13 A 0.0186 0.6876 0.2938 14 V 0.0425 0.2828 0.6747 15 D 0.0459 0.0837 0.8704 16 E 0.0897 0.0952 0.8150 17 S 0.1471 0.1262 0.7267 18 A 0.2703 0.1433 0.5864 19 R 0.4531 0.1329 0.4140 20 I 0.5708 0.2118 0.2173 21 E 0.6466 0.1664 0.1870 22 A 0.6206 0.1795 0.1999 23 K 0.4952 0.2486 0.2562 24 R 0.2933 0.3136 0.3930 25 A 0.1306 0.2339 0.6355 26 S 0.0561 0.1124 0.8315 27 D 0.0539 0.0801 0.8660 28 M 0.0887 0.0501 0.8611 29 G 0.0759 0.1496 0.7744 30 K 0.0179 0.5571 0.4250 31 S 0.0306 0.6041 0.3654 32 V 0.0314 0.7868 0.1818 33 M 0.0870 0.7478 0.1651 34 E 0.0689 0.7684 0.1627 35 T 0.1261 0.7474 0.1266 36 V 0.1193 0.7494 0.1314 37 I 0.1422 0.7278 0.1300 38 A 0.1498 0.7001 0.1501 39 F 0.2495 0.5233 0.2271 40 A 0.2300 0.3742 0.3957 41 N 0.1663 0.1505 0.6832 42 E 0.0875 0.0890 0.8235 43 P 0.0495 0.0971 0.8534 44 G 0.0488 0.0812 0.8700 45 L 0.1007 0.0888 0.8105 46 D 0.1201 0.0638 0.8161 47 G 0.1728 0.0555 0.7717 48 G 0.3670 0.0178 0.6152 49 Y 0.8205 0.0053 0.1742 50 L 0.9140 0.0038 0.0821 51 L 0.9150 0.0064 0.0786 52 L 0.8764 0.0173 0.1063 53 G 0.8452 0.0086 0.1462 54 V 0.7844 0.0367 0.1789 55 D 0.6636 0.0489 0.2875 56 W 0.3401 0.1235 0.5364 57 A 0.1266 0.1158 0.7577 58 I 0.0752 0.0734 0.8514 59 N 0.1172 0.0526 0.8302 60 D 0.5688 0.0236 0.4075 61 K 0.7949 0.0112 0.1939 62 G 0.7741 0.0135 0.2123 63 D 0.6832 0.0192 0.2976 64 T 0.5526 0.0459 0.4015 65 V 0.4390 0.0453 0.5157 66 Y 0.2984 0.0683 0.6333 67 R 0.1726 0.0821 0.7453 68 P 0.0910 0.1341 0.7749 69 V 0.0618 0.1593 0.7789 70 G 0.0586 0.1804 0.7610 71 L 0.0460 0.4750 0.4790 72 P 0.0347 0.5792 0.3861 73 D 0.0470 0.6230 0.3300 74 P 0.0136 0.8483 0.1381 75 D 0.0112 0.8920 0.0968 76 K 0.0081 0.9197 0.0722 77 V 0.0065 0.9313 0.0623 78 Q 0.0064 0.9313 0.0623 79 R 0.0065 0.9208 0.0728 80 D 0.0078 0.8949 0.0973 81 L 0.0105 0.8688 0.1207 82 A 0.0146 0.7905 0.1949 83 S 0.0234 0.6574 0.3192 84 Q 0.0200 0.6226 0.3574 85 C 0.0348 0.6198 0.3454 86 A 0.0494 0.5911 0.3595 87 S 0.0545 0.5223 0.4232 88 M 0.1121 0.3354 0.5525 89 L 0.1644 0.1709 0.6647 90 N 0.1299 0.0558 0.8143 91 V 0.1342 0.0779 0.7879 92 A 0.1476 0.0616 0.7908 93 L 0.1958 0.0584 0.7458 94 R 0.1876 0.0376 0.7748 95 P 0.2136 0.0705 0.7159 96 E 0.3867 0.0480 0.5652 97 M 0.6707 0.0146 0.3147 98 Q 0.8340 0.0081 0.1578 99 L 0.8659 0.0053 0.1287 100 E 0.8780 0.0064 0.1156 101 Q 0.8367 0.0059 0.1574 102 V 0.6100 0.0294 0.3606 103 G 0.1015 0.0377 0.8608 104 G 0.0435 0.0493 0.9072 105 K 0.5092 0.0137 0.4771 106 T 0.8742 0.0035 0.1223 107 L 0.9258 0.0033 0.0708 108 L 0.9313 0.0032 0.0655 109 V 0.9283 0.0034 0.0683 110 V 0.9145 0.0047 0.0809 111 Y 0.8653 0.0044 0.1303 112 V 0.6010 0.0080 0.3910 113 P 0.2477 0.0199 0.7324 114 E 0.0887 0.0880 0.8233 115 A 0.1011 0.0593 0.8396 116 D 0.0813 0.0608 0.8579 117 V 0.0304 0.3050 0.6646 118 T 0.0380 0.2236 0.7384 119 H 0.1119 0.1349 0.7532 120 K 0.2362 0.0230 0.7408 121 P 0.3441 0.0132 0.6427 122 I 0.7703 0.0151 0.2146 123 Y 0.8507 0.0080 0.1413 124 K 0.7705 0.0169 0.2126 125 K 0.5760 0.0322 0.3918 126 A 0.2909 0.0571 0.6520 127 T 0.1326 0.0637 0.8038 128 G 0.1234 0.0751 0.8015 129 L 0.1746 0.0824 0.7429 130 P 0.1927 0.1039 0.7034 131 G 0.1687 0.0643 0.7670 132 G 0.2795 0.0374 0.6832 133 A 0.6291 0.0172 0.3537 134 Y 0.8404 0.0092 0.1504 135 R 0.8448 0.0107 0.1445 136 R 0.7487 0.0114 0.2400 137 I 0.4692 0.0533 0.4775 138 G 0.1198 0.0516 0.8286 139 S 0.0682 0.0665 0.8653 140 S 0.0870 0.0894 0.8235 141 D 0.1501 0.0892 0.7607 142 Q 0.2409 0.1165 0.6427 143 R 0.2979 0.1064 0.5957 144 C 0.1620 0.0624 0.7756 145 V 0.0466 0.0306 0.9229