# This file is the result of combining several RDB files, specifically # T0318.t06.dssp-ebghstl.rdb (weight 1.53986) # T0318.t06.stride-ebghtl.rdb (weight 1.24869) # T0318.t06.str2.rdb (weight 1.54758) # T0318.t06.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 T0318.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0318 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0318.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2 # # ============================================ # Comments from T0318.t06.stride-ebghtl.rdb # ============================================ # TARGET T0318 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0318.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2 # # ============================================ # Comments from T0318.t06.str2.rdb # ============================================ # TARGET T0318 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0318.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2 # # ============================================ # Comments from T0318.t06.alpha.rdb # ============================================ # TARGET T0318 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0318.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1209 0.0984 0.7807 2 T 0.3757 0.1373 0.4870 3 Q 0.6604 0.1494 0.1902 4 V 0.7431 0.1472 0.1097 5 L 0.7484 0.1626 0.0890 6 V 0.6969 0.1783 0.1248 7 R 0.5026 0.2669 0.2305 8 N 0.1723 0.2680 0.5597 9 G 0.1453 0.2081 0.6466 10 I 0.3833 0.2371 0.3795 11 Q 0.4466 0.2960 0.2574 12 A 0.4725 0.2740 0.2535 13 V 0.2930 0.2727 0.4342 14 G 0.1428 0.1408 0.7164 15 D 0.0815 0.1573 0.7612 16 G 0.1161 0.1014 0.7825 17 L 0.3235 0.0528 0.6236 18 T 0.4549 0.0530 0.4921 19 S 0.7979 0.0239 0.1781 20 L 0.8989 0.0155 0.0856 21 I 0.9107 0.0155 0.0738 22 I 0.8908 0.0195 0.0897 23 V 0.6696 0.0644 0.2660 24 G 0.3525 0.0392 0.6083 25 K 0.2538 0.1739 0.5723 26 K 0.2048 0.3907 0.4045 27 S 0.3011 0.3626 0.3364 28 V 0.3336 0.4122 0.2542 29 L 0.3721 0.3747 0.2532 30 K 0.3274 0.3910 0.2816 31 N 0.3566 0.3170 0.3264 32 V 0.5022 0.1633 0.3345 33 T 0.4788 0.1550 0.3662 34 F 0.4170 0.1929 0.3901 35 E 0.2192 0.2525 0.5283 36 G 0.1378 0.2469 0.6153 37 K 0.1976 0.3684 0.4340 38 F 0.1474 0.6690 0.1837 39 K 0.0814 0.8149 0.1037 40 E 0.1340 0.7669 0.0991 41 V 0.1195 0.7783 0.1022 42 A 0.1469 0.7320 0.1211 43 Q 0.1491 0.7165 0.1345 44 K 0.1180 0.7155 0.1666 45 F 0.1770 0.6019 0.2211 46 V 0.2241 0.3623 0.4136 47 T 0.1618 0.1902 0.6481 48 D 0.0880 0.1055 0.8065 49 G 0.0362 0.1590 0.8048 50 D 0.0592 0.1864 0.7543 51 S 0.1230 0.3106 0.5664 52 W 0.0750 0.6547 0.2703 53 N 0.0758 0.6667 0.2576 54 S 0.1249 0.6393 0.2358 55 M 0.1732 0.6310 0.1959 56 I 0.2443 0.5371 0.2186 57 S 0.2140 0.4596 0.3264 58 R 0.2028 0.3451 0.4520 59 I 0.1880 0.0597 0.7524 60 P 0.1186 0.0611 0.8203 61 A 0.0610 0.2190 0.7200 62 S 0.0471 0.1831 0.7698 63 G 0.0468 0.1102 0.8430 64 R 0.0900 0.0819 0.8281 65 H 0.1079 0.0813 0.8109 66 P 0.0942 0.3921 0.5137 67 L 0.1116 0.5659 0.3224 68 H 0.1810 0.5598 0.2593 69 Y 0.2176 0.6241 0.1583 70 E 0.2852 0.5560 0.1588 71 L 0.2393 0.6110 0.1497 72 A 0.2395 0.5795 0.1809 73 H 0.2239 0.5858 0.1903 74 L 0.3108 0.4935 0.1957 75 I 0.4040 0.3209 0.2750 76 T 0.3990 0.2096 0.3914 77 V 0.2374 0.0709 0.6917 78 P 0.1449 0.0890 0.7661 79 D 0.1151 0.1358 0.7490 80 A 0.0645 0.3216 0.6139 81 S 0.0632 0.2782 0.6587 82 S 0.1008 0.1987 0.7006 83 R 0.1050 0.1102 0.7848 84 G 0.0941 0.0613 0.8447 85 N 0.1116 0.0472 0.8412 86 T 0.1023 0.0345 0.8632 87 P 0.1058 0.0755 0.8187 88 T 0.1033 0.1636 0.7331 89 N 0.0839 0.2406 0.6756 90 A 0.0432 0.5755 0.3813 91 H 0.0518 0.6483 0.3000 92 S 0.1025 0.6766 0.2209 93 I 0.1264 0.6852 0.1884 94 Y 0.1140 0.6908 0.1952 95 K 0.0981 0.6799 0.2220 96 E 0.0980 0.5725 0.3295 97 L 0.1618 0.3282 0.5101 98 K 0.1384 0.1024 0.7591 99 P 0.1866 0.0805 0.7329 100 I 0.2081 0.0516 0.7403 101 N 0.1900 0.0482 0.7618 102 Y 0.1263 0.0229 0.8507 103 P 0.0747 0.1381 0.7872 104 E 0.0442 0.2531 0.7026 105 D 0.0679 0.2233 0.7089 106 T 0.1285 0.2110 0.6606 107 K 0.1647 0.1591 0.6762 108 N 0.2841 0.0674 0.6484 109 V 0.5890 0.0186 0.3925 110 H 0.8085 0.0178 0.1737 111 F 0.9148 0.0116 0.0735 112 V 0.9037 0.0214 0.0749 113 L 0.8639 0.0400 0.0961 114 F 0.7305 0.0625 0.2071 115 A 0.4206 0.1172 0.4621 116 E 0.2053 0.1526 0.6421 117 Y 0.1191 0.1958 0.6852 118 P 0.0197 0.6473 0.3330 119 D 0.0174 0.7845 0.1981 120 V 0.0092 0.9087 0.0820 121 L 0.0067 0.9348 0.0585 122 S 0.0062 0.9346 0.0593 123 H 0.0068 0.9408 0.0524 124 V 0.0053 0.9533 0.0414 125 A 0.0051 0.9538 0.0411 126 A 0.0063 0.9477 0.0460 127 I 0.0074 0.9340 0.0587 128 A 0.0105 0.9038 0.0857 129 R 0.0157 0.8650 0.1194 130 T 0.0320 0.8030 0.1649 131 F 0.0612 0.7059 0.2328 132 C 0.1141 0.5604 0.3255 133 K 0.1248 0.5418 0.3334 134 F 0.1683 0.4590 0.3727 135 S 0.2180 0.3507 0.4313 136 M 0.2399 0.3029 0.4571 137 K 0.2662 0.2229 0.5109 138 T 0.2082 0.1862 0.6055 139 S 0.1354 0.1545 0.7101 140 G 0.1712 0.1540 0.6748 141 I 0.3257 0.1658 0.5084 142 R 0.4059 0.1748 0.4193 143 E 0.5322 0.1701 0.2976 144 L 0.5150 0.1589 0.3261 145 N 0.5218 0.0726 0.4056 146 V 0.5783 0.0442 0.3776 147 N 0.5296 0.0471 0.4233 148 I 0.5273 0.1025 0.3702 149 D 0.5969 0.1222 0.2810 150 V 0.7177 0.1228 0.1594 151 V 0.6369 0.1513 0.2118 152 C 0.4222 0.1976 0.3802 153 D 0.1904 0.2387 0.5709 154 K 0.1556 0.2395 0.6049 155 L 0.1707 0.1836 0.6457 156 T 0.1180 0.1369 0.7451 157 N 0.0605 0.2072 0.7323 158 E 0.0402 0.3611 0.5987 159 D 0.0849 0.3215 0.5936 160 A 0.2297 0.3713 0.3990 161 V 0.4225 0.3550 0.2225 162 F 0.4900 0.3287 0.1813 163 L 0.3954 0.3531 0.2515 164 T 0.2516 0.3563 0.3921 165 D 0.2009 0.3231 0.4760 166 L 0.0859 0.4272 0.4869 167 S 0.0642 0.4723 0.4635 168 E 0.0321 0.7059 0.2620 169 S 0.0465 0.7333 0.2202 170 V 0.0415 0.8194 0.1391 171 R 0.0378 0.8340 0.1282 172 E 0.0446 0.8298 0.1256 173 T 0.0469 0.8107 0.1424 174 A 0.0839 0.7085 0.2076 175 R 0.1114 0.5986 0.2901 176 L 0.1141 0.4362 0.4498 177 I 0.0539 0.0860 0.8601