# This file is the result of combining several RDB files, specifically # T0160.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0160.t2k.stride-ebghtl.rdb (weight 1.24869) # T0160.t2k.str.rdb (weight 1.53983) # T0160.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 T0160.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0160 # 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 T0160.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 81 # # ============================================ # Comments from T0160.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0160 # 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 T0160.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 81 # # ============================================ # Comments from T0160.t2k.str.rdb # ============================================ # TARGET T0160 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0160.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 81 # # ============================================ # Comments from T0160.t2k.alpha.rdb # ============================================ # TARGET T0160 # 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 T0160.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 81 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0516 0.0336 0.9148 2 S 0.0813 0.0659 0.8528 3 H 0.0899 0.1109 0.7992 4 M 0.0818 0.1667 0.7515 5 A 0.0934 0.1169 0.7897 6 K 0.0901 0.0862 0.8238 7 H 0.0912 0.0720 0.8368 8 E 0.1116 0.0926 0.7958 9 Q 0.1792 0.0625 0.7583 10 I 0.4901 0.0346 0.4753 11 L 0.7987 0.0117 0.1896 12 V 0.8449 0.0075 0.1476 13 L 0.8224 0.0076 0.1700 14 D 0.4047 0.0149 0.5804 15 P 0.0951 0.0758 0.8291 16 P 0.0531 0.1367 0.8102 17 S 0.1205 0.1297 0.7498 18 D 0.4447 0.0311 0.5242 19 L 0.8241 0.0060 0.1699 20 K 0.8647 0.0066 0.1287 21 F 0.8049 0.0082 0.1869 22 K 0.6374 0.0160 0.3466 23 G 0.4371 0.0175 0.5454 24 P 0.2006 0.0355 0.7639 25 F 0.0976 0.0797 0.8228 26 T 0.0607 0.0837 0.8557 27 D 0.1345 0.0566 0.8089 28 V 0.4202 0.0243 0.5555 29 V 0.7443 0.0091 0.2466 30 T 0.8347 0.0068 0.1585 31 T 0.8752 0.0067 0.1181 32 N 0.8994 0.0041 0.0965 33 L 0.9150 0.0041 0.0809 34 K 0.9240 0.0037 0.0723 35 L 0.9135 0.0042 0.0823 36 Q 0.8504 0.0176 0.1319 37 N 0.6399 0.0093 0.3509 38 P 0.1176 0.0825 0.7999 39 S 0.0905 0.0410 0.8686 40 D 0.0677 0.0956 0.8367 41 R 0.1919 0.0438 0.7643 42 K 0.5945 0.0250 0.3804 43 V 0.7887 0.0090 0.2023 44 C 0.8927 0.0052 0.1021 45 F 0.9014 0.0050 0.0935 46 K 0.9179 0.0037 0.0784 47 V 0.8951 0.0046 0.1003 48 K 0.8507 0.0097 0.1396 49 T 0.7159 0.0107 0.2734 50 T 0.2856 0.0544 0.6600 51 A 0.1853 0.0186 0.7960 52 P 0.0960 0.1221 0.7818 53 R 0.1612 0.1297 0.7091 54 R 0.5924 0.0498 0.3577 55 Y 0.7519 0.0156 0.2325 56 C 0.8436 0.0073 0.1491 57 V 0.7952 0.0080 0.1968 58 R 0.5433 0.0112 0.4454 59 P 0.2315 0.0272 0.7412 60 N 0.1411 0.0695 0.7894 61 S 0.2881 0.0707 0.6412 62 G 0.4153 0.0377 0.5470 63 V 0.7300 0.0144 0.2556 64 I 0.7481 0.0089 0.2430 65 D 0.2578 0.0136 0.7286 66 P 0.0360 0.0812 0.8828 67 G 0.0256 0.0489 0.9255 68 S 0.2103 0.0259 0.7638 69 I 0.5823 0.0053 0.4124 70 V 0.8831 0.0045 0.1124 71 Y 0.9131 0.0034 0.0835 72 V 0.9239 0.0036 0.0724 73 S 0.9269 0.0035 0.0696 74 V 0.9223 0.0035 0.0742 75 M 0.8930 0.0047 0.1022 76 L 0.7608 0.0069 0.2323 77 Q 0.4246 0.0138 0.5616 78 P 0.1954 0.0550 0.7496 79 F 0.1402 0.0661 0.7936 80 D 0.1573 0.0740 0.7687 81 Y 0.1662 0.0777 0.7561 82 D 0.1133 0.0570 0.8298 83 P 0.1027 0.1063 0.7910 84 N 0.0870 0.1928 0.7202 85 E 0.1033 0.2092 0.6875 86 K 0.1680 0.1673 0.6647 87 S 0.2513 0.1095 0.6392 88 K 0.2042 0.0682 0.7276 89 H 0.2914 0.0355 0.6731 90 K 0.7787 0.0055 0.2158 91 F 0.9045 0.0039 0.0916 92 M 0.9215 0.0038 0.0747 93 V 0.9262 0.0034 0.0705 94 Q 0.9052 0.0063 0.0886 95 T 0.8957 0.0039 0.1004 96 I 0.8113 0.0100 0.1787 97 F 0.6790 0.0121 0.3089 98 A 0.3004 0.0158 0.6837 99 P 0.1225 0.0337 0.8438 100 P 0.0421 0.1034 0.8545 101 N 0.0442 0.1147 0.8411 102 I 0.0604 0.3175 0.6221 103 S 0.0380 0.4340 0.5280 104 D 0.0467 0.5005 0.4527 105 M 0.0126 0.7989 0.1885 106 E 0.0070 0.8916 0.1013 107 A 0.0063 0.9264 0.0673 108 V 0.0055 0.9278 0.0667 109 W 0.0065 0.9165 0.0770 110 K 0.0067 0.8776 0.1157 111 E 0.0114 0.7749 0.2138 112 A 0.0348 0.5698 0.3954 113 K 0.0472 0.2311 0.7217 114 P 0.0378 0.1321 0.8301 115 D 0.0600 0.0961 0.8439 116 E 0.1589 0.0924 0.7487 117 L 0.3928 0.0671 0.5401 118 M 0.6803 0.0338 0.2860 119 D 0.8175 0.0174 0.1651 120 S 0.8252 0.0145 0.1604 121 K 0.8468 0.0089 0.1444 122 P 0.8273 0.0086 0.1641 123 R 0.8584 0.0049 0.1367 124 C 0.8841 0.0040 0.1119 125 V 0.8831 0.0067 0.1102 126 F 0.8608 0.0056 0.1336 127 E 0.7174 0.0089 0.2737 128 M 0.0867 0.0118 0.9015