# This file is the result of combining several RDB files, specifically # T0211.t04.dssp-ebghstl.rdb (weight 1.53986) # T0211.t04.stride-ebghtl.rdb (weight 1.24869) # T0211.t04.str2.rdb (weight 1.54758) # T0211.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 T0211.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0211 # 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 T0211.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 13.3021 # # ============================================ # Comments from T0211.t04.stride-ebghtl.rdb # ============================================ # TARGET T0211 # 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 T0211.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 13.3021 # # ============================================ # Comments from T0211.t04.str2.rdb # ============================================ # TARGET T0211 # 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 T0211.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 13.3021 # # ============================================ # Comments from T0211.t04.alpha.rdb # ============================================ # TARGET T0211 # 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 T0211.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 13.3021 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0968 0.0338 0.8694 2 R 0.1846 0.0441 0.7712 3 K 0.3002 0.0924 0.6074 4 I 0.3148 0.1270 0.5582 5 D 0.2924 0.1235 0.5840 6 L 0.2228 0.1865 0.5908 7 C 0.2652 0.1710 0.5638 8 L 0.3126 0.1890 0.4985 9 S 0.2522 0.1532 0.5946 10 S 0.2501 0.1808 0.5691 11 E 0.1560 0.1504 0.6936 12 G 0.1617 0.0652 0.7731 13 S 0.3032 0.0289 0.6679 14 E 0.6827 0.0138 0.3035 15 V 0.9030 0.0050 0.0920 16 I 0.9221 0.0043 0.0736 17 L 0.9204 0.0059 0.0737 18 A 0.8631 0.0102 0.1268 19 T 0.5945 0.0154 0.3902 20 S 0.3209 0.0340 0.6451 21 S 0.1230 0.0825 0.7945 22 D 0.0712 0.1093 0.8196 23 E 0.0361 0.1377 0.8262 24 K 0.0392 0.0906 0.8702 25 H 0.1282 0.0252 0.8466 26 P 0.0988 0.0228 0.8784 27 P 0.0509 0.6356 0.3135 28 E 0.0357 0.7108 0.2534 29 N 0.0590 0.7159 0.2251 30 I 0.1745 0.4684 0.3571 31 I 0.2027 0.2824 0.5149 32 D 0.1421 0.1110 0.7469 33 G 0.0628 0.0745 0.8627 34 N 0.1128 0.0129 0.8743 35 P 0.0466 0.3603 0.5931 36 E 0.0648 0.4253 0.5099 37 T 0.2386 0.3941 0.3672 38 F 0.4759 0.2203 0.3038 39 W 0.5325 0.1581 0.3095 40 T 0.5462 0.1125 0.3412 41 T 0.3583 0.0848 0.5569 42 T 0.1531 0.0656 0.7813 43 G 0.0876 0.0501 0.8623 44 M 0.1752 0.0391 0.7856 45 F 0.2363 0.0207 0.7430 46 P 0.3349 0.0198 0.6453 47 Q 0.6211 0.0250 0.3539 48 E 0.8888 0.0054 0.1058 49 F 0.9188 0.0035 0.0777 50 I 0.9308 0.0032 0.0660 51 I 0.9218 0.0033 0.0749 52 C 0.9038 0.0040 0.0922 53 F 0.8538 0.0061 0.1401 54 H 0.7434 0.0187 0.2379 55 K 0.7063 0.0182 0.2755 56 H 0.7185 0.0297 0.2518 57 V 0.7745 0.0131 0.2125 58 R 0.8230 0.0075 0.1695 59 I 0.8424 0.0168 0.1408 60 E 0.7916 0.0351 0.1733 61 R 0.9046 0.0087 0.0866 62 L 0.9181 0.0057 0.0762 63 V 0.9210 0.0057 0.0734 64 I 0.8617 0.0074 0.1308 65 Q 0.7196 0.0280 0.2524 66 S 0.5034 0.0248 0.4719 67 Y 0.3534 0.0339 0.6127 68 F 0.4389 0.0198 0.5413 69 V 0.4447 0.0458 0.5096 70 Q 0.5115 0.0609 0.4276 71 T 0.8287 0.0194 0.1519 72 L 0.8856 0.0044 0.1100 73 K 0.9163 0.0035 0.0802 74 I 0.9076 0.0042 0.0882 75 E 0.7940 0.0105 0.1955 76 K 0.6593 0.0200 0.3207 77 S 0.2788 0.0276 0.6935 78 T 0.1881 0.0410 0.7709 79 S 0.1205 0.0374 0.8421 80 K 0.0726 0.1009 0.8266 81 E 0.1064 0.0812 0.8124 82 P 0.1646 0.1311 0.7043 83 V 0.2119 0.1089 0.6792 84 D 0.3368 0.2013 0.4619 85 F 0.2059 0.6716 0.1225 86 E 0.2075 0.6669 0.1256 87 Q 0.2347 0.6328 0.1325 88 W 0.2416 0.6186 0.1398 89 I 0.2210 0.6187 0.1603 90 E 0.1792 0.6170 0.2037 91 K 0.1504 0.5735 0.2760 92 D 0.1534 0.4584 0.3883 93 L 0.2489 0.2918 0.4593 94 V 0.3235 0.1686 0.5079 95 H 0.2420 0.0793 0.6786 96 T 0.1533 0.1309 0.7158 97 E 0.1885 0.0989 0.7126 98 G 0.4004 0.0597 0.5400 99 Q 0.6234 0.0346 0.3420 100 L 0.7190 0.0167 0.2643 101 Q 0.6076 0.0209 0.3715 102 N 0.2952 0.1690 0.5358 103 E 0.1574 0.4169 0.4257 104 E 0.1920 0.4499 0.3582 105 I 0.2788 0.3901 0.3311 106 V 0.2970 0.2697 0.4332 107 A 0.2193 0.2762 0.5045 108 H 0.1490 0.1602 0.6908 109 D 0.1374 0.0804 0.7822 110 G 0.2273 0.0423 0.7304 111 S 0.4948 0.0336 0.4716 112 A 0.8332 0.0098 0.1570 113 T 0.8760 0.0129 0.1111 114 Y 0.9244 0.0044 0.0712 115 L 0.9154 0.0046 0.0800 116 R 0.9196 0.0048 0.0756 117 F 0.9234 0.0053 0.0713 118 I 0.9153 0.0089 0.0758 119 I 0.9004 0.0111 0.0885 120 V 0.7599 0.0581 0.1820 121 S 0.5300 0.0901 0.3799 122 A 0.1852 0.2135 0.6013 123 F 0.1123 0.2778 0.6100 124 D 0.0577 0.2823 0.6600 125 H 0.0761 0.1950 0.7289 126 F 0.1167 0.1006 0.7827 127 A 0.1890 0.1117 0.6993 128 S 0.3276 0.0921 0.5803 129 V 0.3760 0.1201 0.5039 130 H 0.5609 0.0715 0.3676 131 S 0.7263 0.0473 0.2264 132 V 0.7904 0.0263 0.1833 133 S 0.8530 0.0132 0.1338 134 A 0.8658 0.0092 0.1249 135 E 0.8780 0.0131 0.1089 136 G 0.8804 0.0088 0.1108 137 T 0.8333 0.0128 0.1539 138 V 0.6964 0.0115 0.2921 139 V 0.4804 0.0408 0.4788 140 S 0.2364 0.0809 0.6827 141 N 0.1206 0.0892 0.7902 142 L 0.0802 0.0886 0.8312 143 S 0.0687 0.0553 0.8760 144 S 0.0467 0.0394 0.9139