# This file is the result of combining several RDB files, specifically # T0234.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0234.t2k.stride-ebghtl.rdb (weight 1.24869) # T0234.t2k.str2.rdb (weight 1.54758) # T0234.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 T0234.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0234 # 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 T0234.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 48 # # ============================================ # Comments from T0234.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0234 # 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 T0234.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 48 # # ============================================ # Comments from T0234.t2k.str2.rdb # ============================================ # TARGET T0234 # 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 T0234.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 48 # # ============================================ # Comments from T0234.t2k.alpha.rdb # ============================================ # TARGET T0234 # 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 T0234.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 48 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0496 0.0975 0.8529 2 S 0.1186 0.2350 0.6464 3 Q 0.0940 0.2786 0.6274 4 L 0.0473 0.4612 0.4915 5 E 0.0203 0.5498 0.4299 6 K 0.0274 0.5525 0.4201 7 A 0.0232 0.6570 0.3198 8 Q 0.0110 0.8064 0.1826 9 A 0.0057 0.9336 0.0608 10 E 0.0054 0.9466 0.0481 11 Y 0.0049 0.9483 0.0469 12 A 0.0050 0.9493 0.0457 13 G 0.0054 0.9383 0.0563 14 F 0.0055 0.9269 0.0677 15 I 0.0074 0.8933 0.0993 16 Q 0.0082 0.7635 0.2283 17 E 0.0145 0.5350 0.4505 18 F 0.0637 0.2526 0.6836 19 Q 0.1286 0.1341 0.7373 20 S 0.5405 0.0930 0.3664 21 A 0.7586 0.0547 0.1867 22 I 0.8292 0.0339 0.1370 23 I 0.8386 0.0270 0.1344 24 S 0.7811 0.0212 0.1977 25 T 0.6809 0.0181 0.3010 26 I 0.6497 0.0114 0.3389 27 S 0.2107 0.0167 0.7727 28 E 0.0318 0.1142 0.8540 29 Q 0.0466 0.0228 0.9307 30 G 0.0578 0.0312 0.9110 31 I 0.2163 0.0116 0.7721 32 P 0.5894 0.0126 0.3979 33 N 0.5605 0.0261 0.4135 34 G 0.5991 0.0165 0.3844 35 S 0.6045 0.0137 0.3817 36 Y 0.7242 0.0234 0.2524 37 A 0.7351 0.0206 0.2443 38 P 0.7078 0.0250 0.2672 39 F 0.7444 0.0190 0.2366 40 V 0.7649 0.0169 0.2182 41 I 0.7876 0.0132 0.1992 42 D 0.3119 0.0254 0.6627 43 D 0.0237 0.1190 0.8573 44 A 0.0430 0.0318 0.9252 45 K 0.0430 0.0338 0.9231 46 N 0.2155 0.0127 0.7719 47 I 0.6908 0.0056 0.3036 48 Y 0.8804 0.0091 0.1105 49 I 0.9044 0.0106 0.0849 50 Y 0.8792 0.0149 0.1058 51 V 0.6346 0.0957 0.2698 52 S 0.2185 0.1772 0.6043 53 G 0.0227 0.7859 0.1913 54 L 0.0103 0.8403 0.1494 55 A 0.0113 0.8780 0.1106 56 V 0.0116 0.8668 0.1216 57 H 0.0155 0.8058 0.1788 58 T 0.0217 0.8286 0.1496 59 K 0.0347 0.7367 0.2286 60 N 0.0445 0.6553 0.3003 61 I 0.0371 0.6399 0.3230 62 E 0.0569 0.4579 0.4851 63 A 0.0755 0.3149 0.6096 64 N 0.0816 0.0436 0.8747 65 P 0.0407 0.0998 0.8595 66 L 0.1688 0.0856 0.7456 67 V 0.6675 0.0173 0.3152 68 N 0.8339 0.0150 0.1511 69 V 0.9159 0.0043 0.0798 70 L 0.9045 0.0048 0.0907 71 F 0.8777 0.0055 0.1167 72 V 0.7302 0.0180 0.2519 73 D 0.4389 0.0276 0.5335 74 D 0.1560 0.0545 0.7895 75 E 0.0672 0.1064 0.8264 76 A 0.0719 0.1267 0.8014 77 K 0.0407 0.1795 0.7798 78 T 0.0525 0.1744 0.7730 79 N 0.0570 0.1318 0.8112 80 Q 0.1100 0.1074 0.7827 81 I 0.1062 0.4024 0.4914 82 F 0.1611 0.4017 0.4372 83 A 0.2466 0.3414 0.4120 84 R 0.3129 0.1482 0.5390 85 R 0.3792 0.0950 0.5258 86 R 0.6865 0.0317 0.2818 87 L 0.8271 0.0088 0.1641 88 S 0.8869 0.0055 0.1077 89 F 0.9059 0.0058 0.0883 90 D 0.8843 0.0104 0.1053 91 C 0.8821 0.0067 0.1112 92 T 0.8954 0.0064 0.0983 93 A 0.8841 0.0062 0.1097 94 T 0.8725 0.0062 0.1213 95 L 0.8186 0.0070 0.1744 96 I 0.4868 0.0154 0.4978 97 E 0.1884 0.0433 0.7683 98 R 0.0594 0.0772 0.8634 99 E 0.0410 0.1363 0.8228 100 S 0.0375 0.2495 0.7130 101 Q 0.0117 0.6952 0.2931 102 K 0.0090 0.8022 0.1887 103 W 0.0069 0.8937 0.0994 104 N 0.0051 0.9315 0.0634 105 Q 0.0052 0.9463 0.0485 106 V 0.0052 0.9515 0.0433 107 V 0.0047 0.9554 0.0399 108 D 0.0047 0.9561 0.0392 109 Q 0.0047 0.9562 0.0390 110 F 0.0048 0.9502 0.0450 111 Q 0.0050 0.9390 0.0560 112 E 0.0067 0.8826 0.1107 113 R 0.0155 0.7852 0.1994 114 F 0.0503 0.4222 0.5275 115 G 0.0166 0.6465 0.3369 116 Q 0.0133 0.7457 0.2410 117 I 0.0127 0.8134 0.1739 118 I 0.0176 0.8025 0.1798 119 E 0.0261 0.7324 0.2415 120 V 0.0315 0.6870 0.2816 121 L 0.0521 0.5827 0.3653 122 R 0.0449 0.4372 0.5179 123 G 0.0576 0.2294 0.7130 124 L 0.0847 0.1809 0.7344 125 A 0.0421 0.1551 0.8029 126 D 0.0838 0.1028 0.8134 127 F 0.4965 0.0224 0.4811 128 R 0.7163 0.0422 0.2415 129 I 0.9044 0.0057 0.0899 130 F 0.9021 0.0052 0.0927 131 Q 0.9142 0.0036 0.0822 132 L 0.8640 0.0043 0.1317 133 T 0.7762 0.0055 0.2183 134 P 0.6255 0.0355 0.3390 135 K 0.5247 0.0723 0.4030 136 E 0.6990 0.0365 0.2645 137 G 0.7446 0.0220 0.2333 138 R 0.8514 0.0174 0.1312 139 F 0.8735 0.0153 0.1112 140 V 0.7684 0.0313 0.2003 141 I 0.5353 0.0717 0.3929 142 G 0.3752 0.0829 0.5419 143 F 0.5089 0.0762 0.4149 144 G 0.6368 0.0553 0.3079 145 A 0.7606 0.0331 0.2063 146 A 0.8150 0.0291 0.1559 147 Y 0.8425 0.0218 0.1357 148 H 0.8652 0.0138 0.1210 149 I 0.7280 0.0191 0.2529 150 S 0.3449 0.0190 0.6361 151 G 0.0267 0.3611 0.6122 152 D 0.0221 0.3701 0.6079 153 R 0.0577 0.4695 0.4728 154 L 0.2217 0.3364 0.4420 155 D 0.3793 0.2527 0.3679 156 T 0.4404 0.2196 0.3401 157 L 0.4767 0.1295 0.3938 158 V 0.4365 0.0839 0.4796 159 P 0.4256 0.0843 0.4901 160 I 0.3374 0.1067 0.5559 161 T 0.2452 0.1202 0.6347 162 G 0.1639 0.1290 0.7071 163 D 0.1290 0.1113 0.7597 164 K 0.0857 0.1199 0.7944 165 G 0.0371 0.0447 0.9182