# This file is the result of combining several RDB files, specifically # T0342.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0342.t2k.stride-ebghtl.rdb (weight 1.24869) # T0342.t2k.str2.rdb (weight 1.54758) # T0342.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 T0342.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0342 # 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 T0342.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 109 # # ============================================ # Comments from T0342.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0342 # 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 T0342.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 109 # # ============================================ # Comments from T0342.t2k.str2.rdb # ============================================ # TARGET T0342 # 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 T0342.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 109 # # ============================================ # Comments from T0342.t2k.alpha.rdb # ============================================ # TARGET T0342 # 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 T0342.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 109 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1000 0.0817 0.8183 2 A 0.1200 0.0789 0.8011 3 N 0.1216 0.0814 0.7970 4 S 0.0867 0.1992 0.7141 5 G 0.0985 0.2392 0.6623 6 C 0.1366 0.2644 0.5989 7 K 0.1671 0.2388 0.5941 8 D 0.1545 0.1706 0.6749 9 V 0.1406 0.1424 0.7170 10 T 0.1150 0.1545 0.7305 11 G 0.0873 0.1402 0.7725 12 P 0.0641 0.1523 0.7836 13 D 0.0700 0.1266 0.8034 14 E 0.0744 0.1127 0.8128 15 E 0.1022 0.0886 0.8092 16 S 0.3144 0.0462 0.6393 17 F 0.6499 0.0235 0.3266 18 L 0.8588 0.0137 0.1275 19 Y 0.8931 0.0145 0.0924 20 F 0.8581 0.0217 0.1201 21 A 0.7607 0.0372 0.2020 22 Y 0.4967 0.0772 0.4261 23 G 0.2272 0.1084 0.6645 24 S 0.0961 0.1900 0.7138 25 N 0.0714 0.2077 0.7209 26 L 0.0781 0.1477 0.7742 27 L 0.0692 0.1108 0.8200 28 T 0.0077 0.8781 0.1142 29 E 0.0078 0.9091 0.0831 30 R 0.0078 0.9185 0.0737 31 I 0.0121 0.9104 0.0775 32 H 0.0161 0.8706 0.1133 33 L 0.0197 0.7687 0.2117 34 R 0.0528 0.5261 0.4211 35 N 0.0864 0.1153 0.7983 36 P 0.0361 0.1504 0.8136 37 S 0.0565 0.1147 0.8288 38 A 0.0840 0.1478 0.7682 39 A 0.1911 0.1221 0.6868 40 F 0.3468 0.0975 0.5557 41 F 0.4944 0.0646 0.4410 42 C 0.6581 0.0316 0.3103 43 V 0.8125 0.0211 0.1665 44 A 0.8590 0.0127 0.1284 45 R 0.8797 0.0071 0.1131 46 L 0.7512 0.0146 0.2342 47 Q 0.1062 0.0812 0.8126 48 D 0.0714 0.0466 0.8820 49 F 0.6028 0.0272 0.3700 50 K 0.8267 0.0112 0.1621 51 L 0.8842 0.0088 0.1070 52 D 0.8560 0.0136 0.1304 53 F 0.7429 0.0281 0.2289 54 G 0.3551 0.0485 0.5964 55 N 0.1629 0.0874 0.7497 56 S 0.0974 0.1217 0.7810 57 Q 0.1069 0.1055 0.7876 58 G 0.1562 0.1106 0.7332 59 K 0.2082 0.1541 0.6376 60 T 0.2179 0.1639 0.6183 61 S 0.2235 0.1340 0.6426 62 Q 0.2242 0.1431 0.6327 63 T 0.1953 0.1394 0.6653 64 W 0.1509 0.1286 0.7205 65 H 0.1239 0.1045 0.7717 66 G 0.1595 0.0813 0.7592 67 G 0.3410 0.0571 0.6019 68 I 0.6210 0.0430 0.3360 69 A 0.7104 0.0338 0.2558 70 T 0.7536 0.0191 0.2273 71 I 0.7878 0.0165 0.1957 72 F 0.7692 0.0132 0.2176 73 Q 0.6844 0.0219 0.2937 74 S 0.2335 0.0215 0.7450 75 P 0.0396 0.0803 0.8801 76 G 0.0329 0.0437 0.9234 77 D 0.1999 0.0276 0.7724 78 E 0.6240 0.0128 0.3632 79 V 0.8417 0.0052 0.1531 80 W 0.8575 0.0178 0.1247 81 G 0.8858 0.0057 0.1085 82 V 0.9173 0.0038 0.0789 83 V 0.9122 0.0080 0.0799 84 W 0.8939 0.0073 0.0988 85 K 0.8567 0.0069 0.1364 86 M 0.5287 0.0080 0.4632 87 N 0.1597 0.0133 0.8270 88 K 0.0081 0.7110 0.2809 89 S 0.0058 0.7854 0.2088 90 N 0.0093 0.8296 0.1611 91 L 0.0095 0.8954 0.0951 92 N 0.0061 0.8531 0.1408 93 S 0.0092 0.8346 0.1562 94 L 0.0264 0.8124 0.1613 95 D 0.0293 0.7861 0.1846 96 E 0.0178 0.7929 0.1893 97 Q 0.0262 0.6922 0.2816 98 E 0.0553 0.4223 0.5225 99 G 0.0564 0.1215 0.8221 100 V 0.0910 0.0855 0.8235 101 K 0.1114 0.1132 0.7755 102 S 0.0948 0.2182 0.6870 103 G 0.1285 0.1746 0.6970 104 M 0.3235 0.1164 0.5601 105 Y 0.5370 0.0401 0.4228 106 V 0.5775 0.0254 0.3971 107 V 0.6459 0.0194 0.3346 108 I 0.7380 0.0167 0.2453 109 E 0.8073 0.0087 0.1840 110 V 0.8242 0.0061 0.1697 111 K 0.8470 0.0054 0.1476 112 V 0.8285 0.0083 0.1632 113 A 0.7106 0.0121 0.2773 114 T 0.3785 0.0393 0.5822 115 Q 0.1072 0.0528 0.8400 116 E 0.0685 0.0702 0.8614 117 G 0.1734 0.0574 0.7692 118 K 0.5081 0.0294 0.4626 119 E 0.6949 0.0186 0.2865 120 I 0.7551 0.0185 0.2264 121 T 0.8070 0.0177 0.1753 122 C 0.8546 0.0139 0.1315 123 R 0.8859 0.0095 0.1045 124 S 0.8830 0.0102 0.1068 125 Y 0.8153 0.0185 0.1662 126 L 0.6149 0.0456 0.3395 127 M 0.2923 0.0890 0.6186 128 T 0.1410 0.1429 0.7161 129 N 0.1315 0.0999 0.7686 130 Y 0.0948 0.1357 0.7695 131 E 0.0603 0.1930 0.7467 132 S 0.0533 0.1737 0.7730 133 A 0.0566 0.0888 0.8546 134 P 0.0715 0.0414 0.8871 135 P 0.0838 0.0630 0.8532 136 S 0.0548 0.1112 0.8341 137 P 0.0078 0.8622 0.1300 138 Q 0.0058 0.9071 0.0870 139 Y 0.0053 0.9398 0.0549 140 K 0.0047 0.9574 0.0379 141 K 0.0047 0.9597 0.0355 142 I 0.0047 0.9606 0.0348 143 I 0.0047 0.9602 0.0351 144 C 0.0048 0.9584 0.0369 145 M 0.0052 0.9519 0.0429 146 G 0.0051 0.9492 0.0458 147 A 0.0049 0.9465 0.0486 148 K 0.0055 0.9370 0.0575 149 E 0.0078 0.8513 0.1410 150 N 0.0450 0.4060 0.5491 151 G 0.0450 0.0443 0.9106 152 L 0.0540 0.0120 0.9340 153 P 0.0555 0.0217 0.9229 154 L 0.0056 0.9080 0.0864 155 E 0.0051 0.9432 0.0518 156 Y 0.0050 0.9494 0.0455 157 Q 0.0050 0.9563 0.0387 158 E 0.0059 0.9506 0.0435 159 K 0.0052 0.9392 0.0556 160 L 0.0073 0.9221 0.0706 161 K 0.0084 0.8718 0.1198 162 A 0.0152 0.7088 0.2760 163 I 0.0641 0.4462 0.4897 164 E 0.0948 0.2782 0.6270 165 P 0.0877 0.2421 0.6702 166 N 0.0897 0.1906 0.7197 167 D 0.0743 0.1237 0.8020 168 Y 0.0789 0.0983 0.8228 169 T 0.0464 0.1394 0.8142 170 G 0.0442 0.1053 0.8506 171 K 0.0766 0.1466 0.7767 172 V 0.0986 0.2600 0.6415 173 S 0.0772 0.4003 0.5225 174 E 0.0435 0.7107 0.2458 175 E 0.0220 0.8182 0.1598 176 I 0.0211 0.8626 0.1163 177 E 0.0195 0.8965 0.0840 178 D 0.0130 0.9140 0.0731 179 I 0.0103 0.9146 0.0752 180 I 0.0121 0.8829 0.1049 181 K 0.0157 0.7733 0.2110 182 K 0.0464 0.4747 0.4788 183 G 0.0516 0.1656 0.7828 184 E 0.0859 0.1911 0.7230 185 T 0.1927 0.1417 0.6656 186 Q 0.2597 0.1010 0.6393 187 T 0.2333 0.0665 0.7003 188 L 0.0541 0.0352 0.9107