# This file is the result of combining several RDB files, specifically # T0226.t04.dssp-ebghstl.rdb (weight 1.53986) # T0226.t04.stride-ebghtl.rdb (weight 1.24869) # T0226.t04.str2.rdb (weight 1.54758) # T0226.t04.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.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0226 # Using neural net t04-2621-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 T0226.t04-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 1 # # ============================================ # Comments from T0226.t04.stride-ebghtl.rdb # ============================================ # TARGET T0226 # Using neural net t04-2621-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 T0226.t04-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 1 # # ============================================ # Comments from T0226.t04.str2.rdb # ============================================ # TARGET T0226 # Using neural net t04-2621-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 T0226.t04-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 1 # # ============================================ # Comments from T0226.t04.alpha.rdb # ============================================ # TARGET T0226 # Using neural net t04-2621-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 T0226.t04-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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1224 0.2105 0.6671 2 R 0.1420 0.2255 0.6325 3 D 0.1486 0.1797 0.6716 4 L 0.1087 0.1782 0.7130 5 D 0.0998 0.1186 0.7816 6 R 0.0389 0.4879 0.4732 7 E 0.0760 0.4509 0.4732 8 E 0.1757 0.3930 0.4313 9 T 0.3474 0.2944 0.3582 10 Y 0.5483 0.2192 0.2325 11 L 0.6407 0.1878 0.1716 12 V 0.5976 0.1800 0.2224 13 D 0.4137 0.1834 0.4029 14 R 0.1517 0.3384 0.5099 15 T 0.1172 0.2937 0.5891 16 G 0.1454 0.3059 0.5487 17 L 0.3126 0.3535 0.3339 18 A 0.4606 0.3359 0.2036 19 L 0.4363 0.3451 0.2186 20 E 0.4212 0.3430 0.2358 21 L 0.2266 0.5843 0.1891 22 R 0.1621 0.6453 0.1926 23 D 0.1485 0.6468 0.2048 24 L 0.1502 0.6010 0.2489 25 V 0.1903 0.3988 0.4109 26 G 0.1630 0.1384 0.6987 27 T 0.1565 0.0640 0.7795 28 G 0.1182 0.0271 0.8548 29 P 0.1215 0.0287 0.8499 30 V 0.1182 0.0182 0.8636 31 P 0.0936 0.0633 0.8431 32 G 0.0739 0.1050 0.8212 33 E 0.1437 0.1170 0.7394 34 A 0.2165 0.0986 0.6849 35 Y 0.1521 0.0381 0.8098 36 P 0.1113 0.0518 0.8369 37 G 0.0813 0.0411 0.8777 38 P 0.0835 0.2114 0.7051 39 H 0.1061 0.3908 0.5032 40 A 0.1518 0.4129 0.4353 41 A 0.1901 0.4090 0.4009 42 L 0.1781 0.2893 0.5326 43 G 0.1266 0.1261 0.7473 44 Y 0.1165 0.1204 0.7631 45 G 0.1055 0.1194 0.7751 46 E 0.0567 0.4258 0.5175 47 G 0.0675 0.4849 0.4475 48 Q 0.0932 0.7003 0.2065 49 F 0.0799 0.8242 0.0959 50 A 0.0711 0.8398 0.0890 51 A 0.0818 0.8279 0.0904 52 L 0.0844 0.8126 0.1030 53 L 0.1011 0.7268 0.1720 54 S 0.0611 0.5086 0.4302 55 G 0.0521 0.2297 0.7182 56 L 0.0880 0.0350 0.8770 57 P 0.0709 0.1067 0.8224 58 D 0.0827 0.1488 0.7685 59 W 0.0920 0.1983 0.7097 60 G 0.0737 0.1243 0.8020 61 E 0.1341 0.1712 0.6946 62 E 0.1498 0.1280 0.7222 63 G 0.2156 0.0632 0.7213 64 T 0.5008 0.0487 0.4504 65 L 0.8190 0.0279 0.1531 66 F 0.8636 0.0260 0.1104 67 L 0.8634 0.0308 0.1058 68 L 0.7720 0.0467 0.1812 69 E 0.4949 0.0899 0.4153 70 G 0.1751 0.0645 0.7604 71 G 0.1660 0.0788 0.7551 72 Y 0.2459 0.1015 0.6526 73 D 0.2473 0.1480 0.6048 74 L 0.0637 0.6169 0.3193 75 G 0.0500 0.6192 0.3307 76 E 0.0421 0.7493 0.2087 77 A 0.0391 0.8187 0.1422 78 A 0.0454 0.7607 0.1939 79 G 0.0421 0.7143 0.2436 80 M 0.0580 0.8078 0.1342 81 A 0.0661 0.8454 0.0885 82 L 0.0839 0.8380 0.0782 83 L 0.1022 0.8033 0.0945 84 A 0.0705 0.7984 0.1311 85 E 0.0744 0.6901 0.2355 86 T 0.0856 0.3141 0.6003 87 G 0.0791 0.0844 0.8366 88 R 0.2386 0.0813 0.6801 89 A 0.5736 0.0423 0.3841 90 R 0.7466 0.0245 0.2289 91 V 0.8829 0.0114 0.1057 92 V 0.8876 0.0113 0.1011 93 R 0.8896 0.0100 0.1004 94 V 0.7762 0.0288 0.1950 95 G 0.5750 0.0237 0.4013 96 F 0.5095 0.0242 0.4663 97 R 0.3312 0.0243 0.6445 98 P 0.1031 0.0610 0.8359 99 G 0.1291 0.0415 0.8294 100 V 0.6215 0.0145 0.3639 101 E 0.7867 0.0089 0.2044 102 V 0.8434 0.0068 0.1498 103 H 0.8001 0.0076 0.1923 104 I 0.4507 0.0120 0.5372 105 P 0.1706 0.0133 0.8161 106 P 0.0892 0.0519 0.8589 107 S 0.0751 0.0573 0.8676 108 P 0.0471 0.1716 0.7813 109 L 0.0639 0.1525 0.7836 110 A 0.0745 0.0775 0.8480 111 P 0.0669 0.2497 0.6834 112 Y 0.1194 0.4181 0.4625 113 R 0.1480 0.5333 0.3188 114 Y 0.2447 0.5716 0.1837 115 L 0.3879 0.4489 0.1632 116 R 0.4224 0.4355 0.1421 117 F 0.5307 0.3766 0.0927 118 L 0.5028 0.3975 0.0998 119 L 0.5139 0.3527 0.1334 120 L 0.4340 0.2810 0.2850 121 A 0.2528 0.1387 0.6084 122 T 0.0918 0.0627 0.8455