# This file is the result of combining several RDB files, specifically # T0331.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0331.t2k.stride-ebghtl.rdb (weight 1.24869) # T0331.t2k.str2.rdb (weight 1.54758) # T0331.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 T0331.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0331 # 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 T0331.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 97 # # ============================================ # Comments from T0331.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0331 # 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 T0331.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 97 # # ============================================ # Comments from T0331.t2k.str2.rdb # ============================================ # TARGET T0331 # 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 T0331.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 97 # # ============================================ # Comments from T0331.t2k.alpha.rdb # ============================================ # TARGET T0331 # 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 T0331.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 97 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0324 0.4083 0.5593 2 E 0.0442 0.6313 0.3246 3 L 0.0142 0.8446 0.1412 4 K 0.0119 0.8917 0.0965 5 D 0.0118 0.8961 0.0920 6 I 0.0127 0.8930 0.0944 7 M 0.0144 0.8646 0.1210 8 H 0.0181 0.7822 0.1997 9 I 0.0222 0.6641 0.3136 10 L 0.0509 0.4446 0.5045 11 E 0.0284 0.3520 0.6196 12 D 0.0687 0.1475 0.7838 13 M 0.0750 0.0768 0.8482 14 K 0.1064 0.0677 0.8260 15 V 0.6864 0.0215 0.2921 16 G 0.8539 0.0092 0.1369 17 V 0.8945 0.0048 0.1007 18 F 0.8868 0.0078 0.1054 19 A 0.8508 0.0094 0.1398 20 T 0.7893 0.0077 0.2029 21 L 0.7704 0.0073 0.2222 22 D 0.2625 0.0140 0.7235 23 E 0.0237 0.1107 0.8656 24 Y 0.0479 0.0184 0.9337 25 G 0.0655 0.0246 0.9099 26 N 0.1852 0.0120 0.8029 27 P 0.5480 0.0149 0.4371 28 H 0.5743 0.0352 0.3905 29 A 0.7573 0.0126 0.2302 30 R 0.8211 0.0070 0.1719 31 H 0.8763 0.0077 0.1160 32 A 0.8991 0.0059 0.0950 33 H 0.9024 0.0074 0.0902 34 I 0.8856 0.0130 0.1015 35 T 0.8471 0.0273 0.1256 36 A 0.8215 0.0269 0.1516 37 A 0.6956 0.0562 0.2481 38 N 0.4496 0.0523 0.4982 39 E 0.1142 0.0915 0.7943 40 E 0.0878 0.0416 0.8705 41 G 0.4394 0.0178 0.5429 42 I 0.8303 0.0045 0.1652 43 F 0.9076 0.0048 0.0876 44 F 0.9094 0.0042 0.0863 45 M 0.8599 0.0065 0.1336 46 T 0.6000 0.0158 0.3842 47 S 0.1576 0.0565 0.7859 48 P 0.0339 0.1462 0.8198 49 E 0.0301 0.1674 0.8026 50 T 0.0683 0.2496 0.6821 51 H 0.0918 0.4579 0.4503 52 F 0.1088 0.6123 0.2788 53 Y 0.0994 0.7687 0.1319 54 D 0.1084 0.7861 0.1055 55 Q 0.0852 0.8148 0.1000 56 L 0.0604 0.8167 0.1230 57 M 0.0494 0.6926 0.2580 58 G 0.0412 0.4553 0.5035 59 D 0.0920 0.0443 0.8637 60 Q 0.0440 0.0858 0.8701 61 R 0.3084 0.0447 0.6468 62 V 0.8687 0.0052 0.1262 63 A 0.9094 0.0065 0.0841 64 M 0.9247 0.0036 0.0717 65 T 0.9085 0.0046 0.0869 66 A 0.8239 0.0067 0.1694 67 I 0.6546 0.0174 0.3280 68 S 0.3349 0.0206 0.6445 69 E 0.0920 0.0616 0.8463 70 E 0.0357 0.1771 0.7872 71 G 0.0352 0.2160 0.7488 72 Y 0.0962 0.2485 0.6553 73 L 0.3051 0.1874 0.5075 74 I 0.4297 0.1123 0.4580 75 Q 0.5967 0.0471 0.3562 76 V 0.8314 0.0107 0.1579 77 V 0.8852 0.0069 0.1080 78 R 0.9157 0.0037 0.0806 79 V 0.9039 0.0056 0.0905 80 E 0.8464 0.0194 0.1342 81 G 0.8018 0.0100 0.1882 82 T 0.8478 0.0098 0.1424 83 A 0.8437 0.0082 0.1480 84 R 0.8220 0.0076 0.1703 85 P 0.7517 0.0091 0.2392 86 V 0.4376 0.0132 0.5492 87 E 0.1809 0.0220 0.7971 88 N 0.0266 0.6624 0.3110 89 D 0.0074 0.8769 0.1157 90 Y 0.0069 0.9047 0.0885 91 L 0.0068 0.9105 0.0827 92 K 0.0079 0.9183 0.0738 93 T 0.0090 0.9158 0.0752 94 V 0.0078 0.9072 0.0850 95 F 0.0136 0.8646 0.1218 96 A 0.0133 0.7636 0.2231 97 D 0.0190 0.6015 0.3795 98 N 0.0525 0.1645 0.7830 99 P 0.0511 0.1598 0.7891 100 Y 0.0414 0.3556 0.6030 101 Y 0.0409 0.5287 0.4304 102 Q 0.0658 0.4758 0.4584 103 H 0.1322 0.4155 0.4523 104 I 0.1862 0.3199 0.4939 105 Y 0.1873 0.2700 0.5427 106 K 0.2271 0.2678 0.5051 107 D 0.2287 0.2021 0.5692 108 E 0.1795 0.1716 0.6489 109 S 0.1267 0.1046 0.7686 110 S 0.0687 0.2053 0.7261 111 D 0.0738 0.2065 0.7197 112 T 0.1560 0.2051 0.6389 113 M 0.2807 0.1687 0.5506 114 Q 0.3666 0.2000 0.4335 115 V 0.2688 0.3334 0.3978 116 F 0.1547 0.4417 0.4036 117 Q 0.0958 0.4996 0.4046 118 I 0.0148 0.8652 0.1200 119 Y 0.0100 0.9048 0.0853 120 A 0.0069 0.9274 0.0657 121 G 0.0057 0.9414 0.0530 122 H 0.0056 0.9471 0.0473 123 G 0.0055 0.9480 0.0465 124 F 0.0051 0.9435 0.0513 125 Y 0.0058 0.9384 0.0557 126 H 0.0065 0.9251 0.0684 127 S 0.0067 0.8990 0.0943 128 L 0.0089 0.8605 0.1306 129 T 0.0148 0.8015 0.1837 130 Q 0.0192 0.7065 0.2743 131 G 0.0352 0.5706 0.3942 132 H 0.0783 0.2569 0.6648 133 K 0.0477 0.1464 0.8060 134 Y 0.0546 0.1152 0.8302 135 I 0.0886 0.0729 0.8385 136 F 0.1424 0.0386 0.8190 137 S 0.1852 0.0210 0.7938 138 I 0.1324 0.0174 0.8502 139 G 0.1347 0.0267 0.8386 140 Q 0.0821 0.0644 0.8535 141 G 0.0532 0.1672 0.7796 142 E 0.1314 0.1596 0.7091 143 H 0.2333 0.0983 0.6685 144 S 0.2725 0.0681 0.6594 145 E 0.4267 0.0461 0.5272 146 V 0.6621 0.0214 0.3165 147 R 0.7661 0.0095 0.2244 148 A 0.6740 0.0071 0.3189 149 L 0.0961 0.0155 0.8883