# This file is the result of combining several RDB files, specifically # T0226.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0226.t2k.stride-ebghtl.rdb (weight 1.24869) # T0226.t2k.str2.rdb (weight 1.54758) # T0226.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 T0226.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0226 # 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 T0226.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 1 # # ============================================ # Comments from T0226.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0226 # 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 T0226.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 1 # # ============================================ # Comments from T0226.t2k.str2.rdb # ============================================ # TARGET T0226 # 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 T0226.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 1 # # ============================================ # Comments from T0226.t2k.alpha.rdb # ============================================ # TARGET T0226 # 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 T0226.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0557 0.0608 0.8836 2 R 0.0904 0.1463 0.7633 3 D 0.0965 0.2017 0.7018 4 L 0.0735 0.2638 0.6627 5 D 0.0969 0.2363 0.6668 6 R 0.0946 0.3399 0.5655 7 E 0.1333 0.3417 0.5250 8 E 0.1842 0.3448 0.4710 9 T 0.2585 0.3103 0.4312 10 Y 0.3970 0.2622 0.3408 11 L 0.4744 0.2475 0.2781 12 V 0.4328 0.2497 0.3175 13 D 0.3109 0.2273 0.4618 14 R 0.1615 0.3354 0.5032 15 T 0.1175 0.3046 0.5780 16 G 0.1888 0.2312 0.5801 17 L 0.3526 0.2474 0.4001 18 A 0.4815 0.2689 0.2496 19 L 0.4578 0.3254 0.2168 20 E 0.4444 0.3228 0.2327 21 L 0.2931 0.4839 0.2229 22 R 0.2298 0.5327 0.2375 23 D 0.2152 0.5065 0.2783 24 L 0.2096 0.4616 0.3288 25 V 0.2268 0.3034 0.4698 26 G 0.1668 0.1718 0.6614 27 T 0.1359 0.1031 0.7610 28 G 0.1386 0.0595 0.8020 29 P 0.1806 0.0618 0.7576 30 V 0.1770 0.0521 0.7710 31 P 0.1224 0.1129 0.7648 32 G 0.0879 0.1585 0.7536 33 E 0.1185 0.2039 0.6776 34 A 0.1737 0.1689 0.6574 35 Y 0.1635 0.1043 0.7323 36 P 0.1248 0.1227 0.7525 37 G 0.1056 0.1210 0.7734 38 P 0.0845 0.2870 0.6285 39 H 0.1129 0.3750 0.5120 40 A 0.1269 0.4502 0.4229 41 A 0.1622 0.4313 0.4065 42 L 0.1359 0.3556 0.5085 43 G 0.1167 0.2352 0.6481 44 Y 0.1044 0.2009 0.6947 45 G 0.0961 0.2084 0.6955 46 E 0.0665 0.4470 0.4865 47 G 0.0624 0.5459 0.3918 48 Q 0.0778 0.6888 0.2335 49 F 0.0890 0.7770 0.1340 50 A 0.0840 0.8057 0.1103 51 A 0.0877 0.7984 0.1139 52 L 0.0743 0.7984 0.1273 53 L 0.0862 0.7188 0.1951 54 S 0.0744 0.4813 0.4444 55 G 0.0739 0.1896 0.7365 56 L 0.1169 0.1006 0.7825 57 P 0.0898 0.1817 0.7286 58 D 0.0758 0.2174 0.7068 59 W 0.0807 0.2432 0.6761 60 G 0.0795 0.1811 0.7394 61 E 0.1235 0.2054 0.6711 62 E 0.1909 0.1646 0.6444 63 G 0.2521 0.0992 0.6487 64 T 0.4965 0.0773 0.4262 65 L 0.7589 0.0575 0.1836 66 F 0.8171 0.0475 0.1354 67 L 0.8178 0.0518 0.1303 68 L 0.6913 0.0823 0.2264 69 E 0.4470 0.1179 0.4351 70 G 0.1734 0.0995 0.7271 71 G 0.1447 0.0998 0.7555 72 Y 0.2417 0.1356 0.6228 73 D 0.2415 0.1775 0.5811 74 L 0.0813 0.4042 0.5145 75 G 0.0684 0.4125 0.5191 76 E 0.0616 0.5612 0.3773 77 A 0.0831 0.6578 0.2591 78 A 0.0769 0.6497 0.2733 79 G 0.1022 0.5413 0.3565 80 M 0.1388 0.6578 0.2034 81 A 0.1873 0.6666 0.1462 82 L 0.2026 0.6661 0.1313 83 L 0.2218 0.6101 0.1681 84 A 0.1705 0.5943 0.2352 85 E 0.1420 0.5378 0.3202 86 T 0.1314 0.2926 0.5759 87 G 0.1302 0.1014 0.7685 88 R 0.2637 0.0922 0.6441 89 A 0.5108 0.0659 0.4233 90 R 0.6891 0.0486 0.2623 91 V 0.8361 0.0231 0.1408 92 V 0.8280 0.0251 0.1469 93 R 0.8198 0.0218 0.1584 94 V 0.6699 0.0442 0.2859 95 G 0.5514 0.0402 0.4084 96 F 0.4793 0.0416 0.4791 97 R 0.2759 0.0334 0.6908 98 P 0.1149 0.0963 0.7888 99 G 0.1082 0.0721 0.8197 100 V 0.4005 0.0333 0.5662 101 E 0.6297 0.0195 0.3508 102 V 0.6797 0.0214 0.2988 103 H 0.5838 0.0213 0.3948 104 I 0.3443 0.0187 0.6370 105 P 0.1590 0.0179 0.8230 106 P 0.0973 0.0912 0.8115 107 S 0.0826 0.1142 0.8032 108 P 0.0682 0.2038 0.7279 109 L 0.0677 0.1993 0.7330 110 A 0.0764 0.1794 0.7443 111 P 0.0783 0.3628 0.5588 112 Y 0.0889 0.5346 0.3765 113 R 0.1095 0.6358 0.2547 114 Y 0.1677 0.6361 0.1962 115 L 0.2035 0.6364 0.1601 116 R 0.2341 0.6263 0.1397 117 F 0.2769 0.5900 0.1331 118 L 0.2740 0.5805 0.1455 119 L 0.2917 0.4853 0.2229 120 L 0.2484 0.3401 0.4115 121 A 0.1376 0.1853 0.6770 122 T 0.0426 0.0379 0.9195