# This file is the result of combining several RDB files, specifically # T0267.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0267.t2k.stride-ebghtl.rdb (weight 1.24869) # T0267.t2k.str2.rdb (weight 1.54758) # T0267.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 T0267.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0267 # 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 T0267.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 966 # # ============================================ # Comments from T0267.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0267 # 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 T0267.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 966 # # ============================================ # Comments from T0267.t2k.str2.rdb # ============================================ # TARGET T0267 # 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 T0267.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 966 # # ============================================ # Comments from T0267.t2k.alpha.rdb # ============================================ # TARGET T0267 # 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 T0267.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 966 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0909 0.0141 0.8950 2 V 0.3991 0.0120 0.5889 3 R 0.5991 0.0153 0.3856 4 I 0.5907 0.0269 0.3824 5 R 0.4853 0.0265 0.4881 6 R 0.3386 0.0332 0.6282 7 A 0.1106 0.0201 0.8693 8 G 0.0662 0.0184 0.9154 9 L 0.0085 0.6518 0.3397 10 E 0.0087 0.6594 0.3319 11 D 0.0226 0.6841 0.2933 12 L 0.0064 0.9154 0.0782 13 P 0.0049 0.9369 0.0582 14 G 0.0050 0.9449 0.0501 15 V 0.0047 0.9548 0.0405 16 A 0.0047 0.9574 0.0379 17 R 0.0048 0.9525 0.0427 18 V 0.0051 0.9464 0.0484 19 L 0.0051 0.9423 0.0526 20 V 0.0056 0.9225 0.0719 21 D 0.0068 0.8878 0.1055 22 T 0.0111 0.8314 0.1575 23 W 0.0266 0.7185 0.2549 24 R 0.0230 0.7058 0.2712 25 A 0.0244 0.6206 0.3550 26 T 0.0392 0.4943 0.4664 27 Y 0.0470 0.4543 0.4987 28 R 0.0423 0.4812 0.4765 29 G 0.0489 0.4652 0.4859 30 V 0.0692 0.4405 0.4903 31 V 0.1053 0.3770 0.5177 32 P 0.0945 0.3786 0.5270 33 E 0.0685 0.4832 0.4483 34 A 0.0635 0.5121 0.4244 35 F 0.0646 0.4895 0.4459 36 L 0.0676 0.4374 0.4950 37 E 0.0660 0.3628 0.5711 38 G 0.0542 0.3914 0.5545 39 L 0.0526 0.3588 0.5886 40 S 0.0529 0.3116 0.6355 41 Y 0.0373 0.5171 0.4456 42 E 0.0193 0.6891 0.2916 43 G 0.0197 0.6895 0.2907 44 Q 0.0198 0.7106 0.2696 45 A 0.0062 0.9087 0.0850 46 E 0.0058 0.9304 0.0639 47 R 0.0053 0.9388 0.0559 48 W 0.0050 0.9403 0.0547 49 A 0.0055 0.9358 0.0588 50 Q 0.0063 0.9089 0.0848 51 R 0.0093 0.8563 0.1344 52 L 0.0224 0.7652 0.2124 53 K 0.0252 0.6068 0.3680 54 T 0.0455 0.3120 0.6425 55 P 0.0453 0.1463 0.8084 56 T 0.0564 0.1195 0.8240 57 W 0.0617 0.1459 0.7925 58 P 0.0815 0.1359 0.7827 59 G 0.2497 0.0789 0.6714 60 R 0.5470 0.0228 0.4302 61 L 0.8392 0.0070 0.1538 62 F 0.9129 0.0034 0.0838 63 V 0.9239 0.0035 0.0726 64 A 0.9098 0.0046 0.0856 65 E 0.9076 0.0047 0.0877 66 S 0.6387 0.0085 0.3528 67 E 0.0531 0.0984 0.8485 68 S 0.0452 0.0228 0.9320 69 G 0.0958 0.0286 0.8755 70 E 0.5640 0.0069 0.4290 71 V 0.9135 0.0029 0.0836 72 V 0.8713 0.0168 0.1119 73 G 0.9170 0.0040 0.0790 74 F 0.9235 0.0037 0.0727 75 A 0.9197 0.0052 0.0751 76 A 0.9187 0.0049 0.0765 77 F 0.8758 0.0099 0.1143 78 G 0.8008 0.0117 0.1875 79 P 0.6543 0.0361 0.3095 80 D 0.3510 0.0667 0.5823 81 R 0.2070 0.0916 0.7014 82 A 0.1260 0.1492 0.7248 83 S 0.0948 0.1902 0.7149 84 G 0.0793 0.2030 0.7177 85 F 0.0833 0.1710 0.7458 86 P 0.1194 0.1397 0.7409 87 G 0.1534 0.1028 0.7438 88 Y 0.2793 0.0746 0.6461 89 T 0.6860 0.0303 0.2837 90 A 0.8433 0.0105 0.1462 91 E 0.8866 0.0061 0.1073 92 L 0.8972 0.0049 0.0979 93 W 0.8310 0.0248 0.1443 94 A 0.8336 0.0133 0.1531 95 I 0.8568 0.0153 0.1279 96 Y 0.8865 0.0075 0.1060 97 V 0.7493 0.0140 0.2367 98 L 0.2889 0.0217 0.6894 99 P 0.0124 0.6763 0.3113 100 T 0.0081 0.7288 0.2631 101 W 0.0126 0.7617 0.2257 102 Q 0.0219 0.5944 0.3837 103 R 0.0339 0.3705 0.5957 104 K 0.0600 0.2569 0.6831 105 G 0.0517 0.2697 0.6786 106 L 0.0267 0.7265 0.2467 107 G 0.0081 0.8869 0.1050 108 R 0.0048 0.9543 0.0408 109 A 0.0047 0.9583 0.0370 110 L 0.0047 0.9579 0.0373 111 F 0.0047 0.9592 0.0361 112 H 0.0049 0.9577 0.0374 113 E 0.0047 0.9574 0.0379 114 G 0.0048 0.9571 0.0381 115 A 0.0048 0.9572 0.0380 116 R 0.0048 0.9564 0.0388 117 L 0.0050 0.9544 0.0406 118 L 0.0054 0.9510 0.0436 119 Q 0.0051 0.9359 0.0589 120 A 0.0076 0.8543 0.1382 121 E 0.0420 0.2602 0.6978 122 G 0.0363 0.0187 0.9450 123 Y 0.0889 0.0106 0.9005 124 G 0.2614 0.0290 0.7096 125 R 0.8398 0.0073 0.1529 126 M 0.9111 0.0051 0.0838 127 L 0.9252 0.0036 0.0711 128 V 0.9112 0.0046 0.0842 129 W 0.8243 0.0054 0.1702 130 V 0.5294 0.0142 0.4564 131 L 0.2293 0.0324 0.7383 132 K 0.0632 0.1166 0.8201 133 E 0.0372 0.1107 0.8522 134 N 0.0560 0.0922 0.8518 135 P 0.0093 0.7856 0.2051 136 K 0.0071 0.8726 0.1202 137 G 0.0051 0.9324 0.0625 138 R 0.0049 0.9534 0.0417 139 G 0.0047 0.9569 0.0384 140 F 0.0050 0.9580 0.0370 141 Y 0.0052 0.9541 0.0406 142 E 0.0055 0.9449 0.0496 143 H 0.0062 0.9098 0.0839 144 L 0.0417 0.4913 0.4669 145 G 0.0477 0.0335 0.9187 146 G 0.1758 0.0202 0.8040 147 V 0.5952 0.0185 0.3863 148 L 0.6783 0.0254 0.2963 149 L 0.5751 0.0591 0.3658 150 G 0.4418 0.0536 0.5046 151 E 0.4966 0.0681 0.4353 152 R 0.5781 0.0392 0.3827 153 E 0.5503 0.0747 0.3750 154 I 0.3951 0.1026 0.5023 155 E 0.2662 0.1305 0.6033 156 L 0.1365 0.1139 0.7496 157 G 0.0635 0.0786 0.8578 158 G 0.0525 0.0532 0.8943 159 A 0.1737 0.0576 0.7687 160 K 0.3302 0.1043 0.5656 161 L 0.3451 0.1776 0.4773 162 W 0.3718 0.2371 0.3911 163 E 0.5109 0.2866 0.2025 164 V 0.6912 0.2031 0.1056 165 A 0.6835 0.2212 0.0953 166 Y 0.6928 0.2009 0.1063 167 G 0.6373 0.2128 0.1499 168 F 0.4996 0.2465 0.2539 169 D 0.3114 0.1931 0.4955 170 L 0.1153 0.1509 0.7338 171 G 0.0565 0.0797 0.8637 172 G 0.0636 0.0770 0.8594 173 H 0.1007 0.0758 0.8235 174 K 0.1489 0.0746 0.7765 175 W 0.0646 0.0319 0.9035