# This file is the result of combining several RDB files, specifically # T0520.t04.dssp-ebghstl.rdb (weight 1.53986) # T0520.t04.stride-ebghtl.rdb (weight 1.24869) # T0520.t04.str2.rdb (weight 1.54758) # T0520.t04.alpha.rdb (weight 0.659012) # T0520.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0520.t2k.stride-ebghtl.rdb (weight 1.24869) # T0520.t2k.str2.rdb (weight 1.54758) # T0520.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 T0520.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0520 # 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 T0520.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 533.191 # # ============================================ # Comments from T0520.t04.stride-ebghtl.rdb # ============================================ # TARGET T0520 # 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 T0520.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 533.191 # # ============================================ # Comments from T0520.t04.str2.rdb # ============================================ # TARGET T0520 # 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 T0520.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 533.191 # # ============================================ # Comments from T0520.t04.alpha.rdb # ============================================ # TARGET T0520 # 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 T0520.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 533.191 # # ============================================ # Comments from T0520.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0520 # 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 T0520.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 2516 # # ============================================ # Comments from T0520.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0520 # 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 T0520.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 2516 # # ============================================ # Comments from T0520.t2k.str2.rdb # ============================================ # TARGET T0520 # 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 T0520.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 2516 # # ============================================ # Comments from T0520.t2k.alpha.rdb # ============================================ # TARGET T0520 # 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 T0520.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 2516 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1305 0.0580 0.8115 2 N 0.1318 0.1219 0.7462 3 A 0.1018 0.1521 0.7461 4 E 0.1560 0.1688 0.6753 5 R 0.3084 0.1166 0.5750 6 R 0.3700 0.0871 0.5429 7 L 0.6210 0.0484 0.3306 8 C 0.8362 0.0192 0.1446 9 A 0.8886 0.0190 0.0923 10 I 0.9130 0.0158 0.0712 11 L 0.8998 0.0230 0.0772 12 A 0.8376 0.0439 0.1186 13 A 0.6681 0.0786 0.2533 14 D 0.4555 0.0798 0.4648 15 M 0.2100 0.3093 0.4807 16 A 0.0998 0.4368 0.4635 17 G 0.0815 0.4497 0.4688 18 Y 0.0645 0.6088 0.3267 19 S 0.0525 0.7119 0.2357 20 R 0.0234 0.8312 0.1454 21 L 0.0159 0.8457 0.1384 22 M 0.0163 0.8065 0.1772 23 E 0.0163 0.6709 0.3128 24 R 0.0254 0.3984 0.5762 25 N 0.0671 0.1441 0.7888 26 E 0.0509 0.0509 0.8982 27 T 0.0071 0.9114 0.0815 28 D 0.0049 0.9443 0.0508 29 V 0.0048 0.9531 0.0421 30 L 0.0047 0.9579 0.0374 31 N 0.0047 0.9599 0.0354 32 R 0.0047 0.9591 0.0362 33 Q 0.0047 0.9578 0.0375 34 K 0.0047 0.9577 0.0375 35 L 0.0048 0.9544 0.0408 36 Y 0.0049 0.9491 0.0460 37 R 0.0050 0.9457 0.0493 38 R 0.0050 0.9476 0.0474 39 E 0.0051 0.9431 0.0517 40 L 0.0050 0.9382 0.0568 41 I 0.0052 0.9456 0.0493 42 D 0.0048 0.9536 0.0416 43 P 0.0048 0.9562 0.0390 44 A 0.0048 0.9559 0.0393 45 I 0.0056 0.9472 0.0473 46 A 0.0077 0.9164 0.0759 47 Q 0.0123 0.8151 0.1726 48 A 0.0456 0.3983 0.5561 49 G 0.0458 0.0371 0.9171 50 G 0.1878 0.0306 0.7815 51 Q 0.7071 0.0191 0.2738 52 I 0.8317 0.0165 0.1518 53 V 0.8035 0.0190 0.1775 54 K 0.7887 0.0155 0.1958 55 T 0.7477 0.0290 0.2232 56 T 0.5442 0.0751 0.3807 57 G 0.3517 0.0849 0.5633 58 D 0.3294 0.0995 0.5711 59 G 0.7225 0.0879 0.1897 60 M 0.7866 0.1055 0.1079 61 L 0.7938 0.1061 0.1002 62 A 0.7614 0.1170 0.1216 63 R 0.6127 0.1402 0.2471 64 F 0.3206 0.0926 0.5867 65 D 0.1311 0.0618 0.8072 66 T 0.0866 0.0562 0.8572 67 A 0.0617 0.1455 0.7928 68 Q 0.0356 0.3310 0.6334 69 A 0.0291 0.4006 0.5703 70 A 0.0195 0.6010 0.3796 71 L 0.0077 0.8277 0.1646 72 R 0.0071 0.8782 0.1147 73 C 0.0061 0.9214 0.0725 74 A 0.0048 0.9504 0.0448 75 L 0.0048 0.9562 0.0391 76 E 0.0048 0.9572 0.0381 77 I 0.0047 0.9585 0.0368 78 Q 0.0047 0.9597 0.0355 79 Q 0.0048 0.9576 0.0376 80 A 0.0048 0.9546 0.0406 81 M 0.0048 0.9523 0.0429 82 Q 0.0050 0.9402 0.0547 83 Q 0.0055 0.9173 0.0772 84 R 0.0073 0.8749 0.1178 85 E 0.0117 0.8311 0.1572 86 E 0.0138 0.7594 0.2268 87 D 0.0212 0.6099 0.3689 88 T 0.0486 0.3466 0.6048 89 P 0.0434 0.2300 0.7267 90 R 0.0388 0.1763 0.7849 91 K 0.0492 0.1284 0.8224 92 E 0.0972 0.0788 0.8241 93 R 0.2473 0.0449 0.7078 94 I 0.5496 0.0140 0.4363 95 Q 0.7935 0.0093 0.1973 96 Y 0.8942 0.0051 0.1008 97 R 0.9012 0.0075 0.0913 98 I 0.8918 0.0073 0.1009 99 G 0.8430 0.0082 0.1488 100 I 0.7779 0.0170 0.2051 101 N 0.6257 0.0330 0.3413 102 I 0.4701 0.0404 0.4894 103 G 0.3562 0.0364 0.6073 104 D 0.4574 0.0492 0.4933 105 I 0.6730 0.0532 0.2739 106 V 0.7384 0.0518 0.2098 107 L 0.6506 0.0619 0.2875 108 E 0.5059 0.0499 0.4442 109 D 0.4763 0.0685 0.4551 110 G 0.2983 0.0774 0.6243 111 D 0.2286 0.0763 0.6952 112 I 0.2991 0.1033 0.5975 113 F 0.2659 0.1603 0.5737 114 G 0.1266 0.2519 0.6215 115 D 0.0563 0.5584 0.3853 116 A 0.0389 0.7692 0.1919 117 V 0.0177 0.9053 0.0770 118 N 0.0136 0.9243 0.0621 119 V 0.0061 0.9492 0.0447 120 A 0.0062 0.9516 0.0422 121 A 0.0064 0.9469 0.0466 122 R 0.0061 0.9371 0.0568 123 L 0.0065 0.9312 0.0623 124 E 0.0087 0.9052 0.0862 125 A 0.0114 0.8607 0.1279 126 I 0.0299 0.7014 0.2687 127 S 0.0649 0.2699 0.6652 128 E 0.0567 0.0787 0.8647 129 P 0.0509 0.1095 0.8395 130 G 0.0670 0.0835 0.8495 131 A 0.5062 0.0342 0.4596 132 I 0.8527 0.0074 0.1399 133 C 0.8654 0.0069 0.1277 134 V 0.6821 0.0119 0.3060 135 S 0.1847 0.0224 0.7929 136 D 0.0054 0.9043 0.0903 137 I 0.0049 0.9393 0.0559 138 V 0.0050 0.9449 0.0501 139 H 0.0049 0.9450 0.0501 140 Q 0.0054 0.9298 0.0648 141 I 0.0069 0.8792 0.1139 142 T 0.0264 0.7423 0.2314 143 Q 0.0245 0.6211 0.3544 144 D 0.0274 0.4822 0.4904 145 R 0.0455 0.3801 0.5744 146 V 0.0617 0.2463 0.6920 147 S 0.1084 0.1432 0.7484 148 E 0.3501 0.0639 0.5860 149 P 0.5612 0.0392 0.3996 150 F 0.6705 0.0367 0.2928 151 T 0.6288 0.0418 0.3294 152 D 0.5580 0.0568 0.3851 153 L 0.3366 0.0624 0.6010 154 G 0.2678 0.0448 0.6874 155 L 0.5006 0.0271 0.4723 156 Q 0.7792 0.0081 0.2127 157 K 0.8092 0.0070 0.1838 158 V 0.6988 0.0142 0.2870 159 K 0.4343 0.0413 0.5244 160 N 0.2006 0.0351 0.7643 161 I 0.1780 0.0444 0.7776 162 T 0.1599 0.0333 0.8067 163 R 0.2098 0.0158 0.7744 164 P 0.4261 0.0077 0.5662 165 I 0.7544 0.0065 0.2390 166 R 0.8732 0.0036 0.1232 167 V 0.9003 0.0042 0.0955 168 W 0.9035 0.0043 0.0922 169 Q 0.8861 0.0045 0.1094 170 W 0.7629 0.0124 0.2248 171 V 0.3958 0.0238 0.5804 172 P 0.1335 0.0547 0.8117 173 D 0.0576 0.1333 0.8092 174 A 0.0598 0.1439 0.7963 175 D 0.0633 0.1848 0.7518 176 R 0.0814 0.1537 0.7649 177 D 0.1108 0.1276 0.7616 178 Q 0.1296 0.0923 0.7781 179 S 0.1038 0.0644 0.8319 180 H 0.0896 0.0743 0.8361 181 D 0.0828 0.0795 0.8376 182 P 0.0764 0.0918 0.8318 183 Q 0.0777 0.1030 0.8192 184 P 0.0749 0.2245 0.7006 185 S 0.0436 0.2745 0.6819 186 H 0.0867 0.2026 0.7107 187 V 0.0565 0.2246 0.7188 188 Q 0.0574 0.1272 0.8154 189 H 0.0564 0.0362 0.9074