# This file is the result of combining several RDB files, specifically # T0302.t04.dssp-ebghstl.rdb (weight 1.53986) # T0302.t04.stride-ebghtl.rdb (weight 1.24869) # T0302.t04.str2.rdb (weight 1.54758) # T0302.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 T0302.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0302 # Using neural net t06-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 T0302.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 386 # # ============================================ # Comments from T0302.t04.stride-ebghtl.rdb # ============================================ # TARGET T0302 # 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 T0302.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 386 # # ============================================ # Comments from T0302.t04.str2.rdb # ============================================ # TARGET T0302 # Using neural net t06-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 T0302.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 386 # # ============================================ # Comments from T0302.t04.alpha.rdb # ============================================ # TARGET T0302 # 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 T0302.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 386 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0630 0.0342 0.9027 2 M 0.1083 0.0182 0.8735 3 V 0.1167 0.0166 0.8667 4 S 0.0770 0.0132 0.9097 5 P 0.0378 0.4498 0.5124 6 E 0.0243 0.7218 0.2539 7 E 0.0408 0.7241 0.2351 8 A 0.0655 0.6748 0.2597 9 V 0.0832 0.6280 0.2888 10 K 0.0768 0.5012 0.4221 11 W 0.0531 0.3237 0.6232 12 G 0.0662 0.1561 0.7777 13 E 0.0872 0.1549 0.7580 14 S 0.0994 0.1790 0.7216 15 F 0.0052 0.9414 0.0534 16 D 0.0047 0.9567 0.0386 17 K 0.0047 0.9551 0.0402 18 L 0.0048 0.9440 0.0512 19 L 0.0070 0.8378 0.1551 20 S 0.0161 0.4374 0.5466 21 H 0.0670 0.0526 0.8805 22 R 0.0061 0.7722 0.2217 23 D 0.0077 0.8065 0.1857 24 G 0.0059 0.9093 0.0848 25 L 0.0047 0.9543 0.0410 26 E 0.0047 0.9597 0.0356 27 A 0.0047 0.9597 0.0356 28 F 0.0047 0.9602 0.0351 29 T 0.0047 0.9605 0.0348 30 R 0.0047 0.9596 0.0357 31 F 0.0047 0.9533 0.0419 32 L 0.0049 0.9225 0.0726 33 K 0.0060 0.8245 0.1695 34 T 0.0138 0.6820 0.3042 35 E 0.0249 0.5532 0.4219 36 F 0.0298 0.3276 0.6427 37 S 0.0343 0.2887 0.6770 38 E 0.0093 0.8449 0.1457 39 E 0.0103 0.8634 0.1263 40 N 0.0117 0.9023 0.0861 41 I 0.0158 0.9141 0.0701 42 E 0.0122 0.9379 0.0499 43 F 0.0243 0.9256 0.0501 44 W 0.0277 0.9272 0.0451 45 I 0.0270 0.9254 0.0476 46 A 0.0213 0.9143 0.0644 47 C 0.0109 0.9027 0.0865 48 E 0.0083 0.9103 0.0815 49 D 0.0135 0.8370 0.1495 50 F 0.0235 0.7461 0.2304 51 K 0.0364 0.5798 0.3838 52 K 0.0471 0.3821 0.5708 53 S 0.0612 0.2289 0.7098 54 K 0.0526 0.1260 0.8214 55 G 0.0574 0.0385 0.9041 56 P 0.0127 0.8246 0.1627 57 Q 0.0101 0.9050 0.0849 58 Q 0.0123 0.9222 0.0654 59 I 0.0075 0.9390 0.0534 60 H 0.0053 0.9522 0.0425 61 L 0.0048 0.9576 0.0376 62 K 0.0047 0.9571 0.0382 63 A 0.0047 0.9600 0.0353 64 K 0.0047 0.9610 0.0344 65 A 0.0046 0.9605 0.0348 66 I 0.0047 0.9586 0.0367 67 Y 0.0048 0.9566 0.0387 68 E 0.0049 0.9508 0.0443 69 K 0.0069 0.9121 0.0810 70 F 0.0091 0.8027 0.1882 71 I 0.0544 0.5769 0.3687 72 Q 0.0540 0.2024 0.7436 73 T 0.0252 0.2183 0.7566 74 D 0.0246 0.0913 0.8841 75 A 0.0819 0.0341 0.8840 76 P 0.1213 0.0626 0.8161 77 K 0.2553 0.0775 0.6672 78 E 0.4360 0.0695 0.4945 79 V 0.5179 0.0442 0.4379 80 N 0.3345 0.0233 0.6422 81 L 0.1158 0.0444 0.8398 82 D 0.0862 0.0687 0.8451 83 F 0.0102 0.7875 0.2023 84 H 0.0123 0.8368 0.1509 85 T 0.0098 0.9197 0.0705 86 K 0.0055 0.9544 0.0401 87 E 0.0050 0.9600 0.0350 88 V 0.0050 0.9580 0.0370 89 I 0.0056 0.9550 0.0394 90 T 0.0071 0.9402 0.0528 91 N 0.0097 0.8865 0.1038 92 S 0.0183 0.7619 0.2198 93 I 0.0467 0.5073 0.4460 94 T 0.0481 0.2806 0.6714 95 Q 0.0612 0.0555 0.8833 96 P 0.0603 0.0612 0.8784 97 T 0.0651 0.0527 0.8822 98 L 0.0142 0.6306 0.3552 99 H 0.0130 0.6867 0.3002 100 S 0.0210 0.7582 0.2208 101 F 0.0077 0.9034 0.0889 102 D 0.0049 0.9550 0.0401 103 A 0.0047 0.9601 0.0352 104 A 0.0047 0.9610 0.0343 105 Q 0.0046 0.9613 0.0341 106 S 0.0046 0.9614 0.0340 107 R 0.0046 0.9603 0.0350 108 V 0.0047 0.9600 0.0353 109 Y 0.0047 0.9597 0.0356 110 Q 0.0047 0.9587 0.0366 111 L 0.0050 0.9517 0.0433 112 M 0.0055 0.9215 0.0731 113 E 0.0075 0.7890 0.2035 114 Q 0.0155 0.6151 0.3694 115 D 0.0395 0.3461 0.6144 116 S 0.0347 0.3785 0.5868 117 Y 0.0380 0.4872 0.4748 118 T 0.0155 0.7263 0.2581 119 R 0.0188 0.7992 0.1820 120 F 0.0179 0.7938 0.1884 121 L 0.0383 0.6567 0.3050 122 K 0.0381 0.4949 0.4669 123 S 0.0622 0.3508 0.5870 124 D 0.0050 0.9065 0.0885 125 I 0.0051 0.9286 0.0663 126 Y 0.0049 0.9470 0.0481 127 L 0.0053 0.9498 0.0449 128 D 0.0064 0.9279 0.0658 129 L 0.0080 0.8752 0.1167 130 M 0.0174 0.7542 0.2284 131 E 0.0232 0.4776 0.4992 132 G 0.0265 0.0832 0.8902