# This file is the result of combining several RDB files, specifically # T0352.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0352.t2k.stride-ebghtl.rdb (weight 1.24869) # T0352.t2k.str2.rdb (weight 1.54758) # T0352.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 T0352.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0352 # 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 T0352.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 57 # # ============================================ # Comments from T0352.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0352 # 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 T0352.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 57 # # ============================================ # Comments from T0352.t2k.str2.rdb # ============================================ # TARGET T0352 # 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 T0352.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 57 # # ============================================ # Comments from T0352.t2k.alpha.rdb # ============================================ # TARGET T0352 # 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 T0352.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 57 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0576 0.0520 0.8905 2 T 0.0896 0.1024 0.8080 3 T 0.0401 0.6392 0.3207 4 H 0.0096 0.8477 0.1427 5 D 0.0061 0.9089 0.0850 6 R 0.0056 0.9279 0.0666 7 V 0.0050 0.9354 0.0596 8 R 0.0048 0.9475 0.0476 9 L 0.0050 0.9439 0.0512 10 Q 0.0050 0.9425 0.0525 11 L 0.0049 0.9508 0.0444 12 Q 0.0049 0.9524 0.0428 13 A 0.0048 0.9529 0.0423 14 L 0.0047 0.9567 0.0386 15 E 0.0047 0.9579 0.0374 16 A 0.0047 0.9585 0.0368 17 L 0.0047 0.9579 0.0374 18 L 0.0048 0.9542 0.0409 19 R 0.0052 0.9358 0.0590 20 E 0.0064 0.8581 0.1355 21 H 0.0448 0.4982 0.4569 22 Q 0.0325 0.1747 0.7928 23 H 0.0433 0.2253 0.7314 24 W 0.0921 0.3165 0.5914 25 R 0.0893 0.3426 0.5682 26 N 0.0986 0.2401 0.6613 27 D 0.0811 0.0668 0.8520 28 E 0.0686 0.0303 0.9011 29 P 0.0764 0.0573 0.8662 30 Q 0.0632 0.1336 0.8031 31 P 0.0087 0.7803 0.2110 32 H 0.0084 0.7935 0.1981 33 Q 0.0173 0.8129 0.1698 34 F 0.0534 0.6120 0.3346 35 N 0.0478 0.3273 0.6249 36 S 0.0714 0.1793 0.7493 37 T 0.0886 0.0911 0.8202 38 Q 0.1062 0.0450 0.8488 39 P 0.1522 0.0891 0.7587 40 F 0.4307 0.0913 0.4780 41 F 0.5384 0.0648 0.3968 42 M 0.4777 0.1093 0.4129 43 D 0.3205 0.1336 0.5458 44 T 0.2749 0.0899 0.6352 45 M 0.2253 0.0317 0.7430 46 E 0.1737 0.0223 0.8040 47 P 0.0233 0.8152 0.1615 48 L 0.0114 0.8970 0.0915 49 E 0.0141 0.9132 0.0728 50 W 0.0175 0.9238 0.0587 51 L 0.0223 0.9196 0.0580 52 Q 0.0179 0.9289 0.0532 53 W 0.0257 0.9164 0.0579 54 V 0.0370 0.8764 0.0866 55 L 0.0512 0.8357 0.1131 56 I 0.0218 0.8361 0.1422 57 P 0.0057 0.9368 0.0576 58 R 0.0055 0.9379 0.0567 59 M 0.0048 0.9535 0.0418 60 H 0.0047 0.9568 0.0385 61 D 0.0051 0.9566 0.0384 62 L 0.0049 0.9551 0.0400 63 L 0.0057 0.9418 0.0525 64 D 0.0071 0.8832 0.1096 65 N 0.0329 0.4251 0.5420 66 K 0.0311 0.0817 0.8872 67 Q 0.0551 0.0234 0.9215 68 P 0.0925 0.0490 0.8585 69 L 0.0811 0.0610 0.8580 70 P 0.0610 0.1000 0.8390 71 G 0.0429 0.2418 0.7154 72 A 0.0981 0.2922 0.6097 73 F 0.1779 0.2187 0.6034 74 A 0.2163 0.2458 0.5379 75 V 0.1730 0.4171 0.4099 76 A 0.0351 0.6417 0.3232 77 P 0.0060 0.9393 0.0546 78 Y 0.0050 0.9481 0.0469 79 Y 0.0050 0.9530 0.0420 80 E 0.0047 0.9551 0.0401 81 M 0.0048 0.9504 0.0448 82 A 0.0053 0.9363 0.0584 83 L 0.0071 0.9009 0.0920 84 A 0.0084 0.8019 0.1898 85 T 0.0145 0.5811 0.4043 86 D 0.0357 0.4346 0.5297 87 H 0.0205 0.5043 0.4752 88 P 0.0110 0.5947 0.3943 89 Q 0.0123 0.6785 0.3092 90 R 0.0097 0.8090 0.1813 91 A 0.0064 0.9048 0.0888 92 L 0.0066 0.9167 0.0767 93 I 0.0052 0.9363 0.0584 94 L 0.0049 0.9455 0.0496 95 A 0.0049 0.9470 0.0481 96 E 0.0048 0.9511 0.0441 97 L 0.0049 0.9446 0.0505 98 E 0.0051 0.9194 0.0755 99 K 0.0063 0.9052 0.0886 100 L 0.0066 0.8967 0.0967 101 D 0.0064 0.9047 0.0889 102 A 0.0078 0.9093 0.0829 103 L 0.0092 0.8962 0.0946 104 F 0.0170 0.8107 0.1723 105 A 0.0289 0.5613 0.4098 106 D 0.0385 0.1910 0.7706 107 D 0.0337 0.3017 0.6646 108 A 0.0244 0.5066 0.4689 109 S 0.0383 0.5445 0.4172 110 L 0.0229 0.7333 0.2438 111 E 0.0302 0.7356 0.2341 112 H 0.0459 0.6565 0.2975 113 H 0.0650 0.5082 0.4267 114 H 0.0899 0.3616 0.5485 115 H 0.0864 0.2310 0.6825 116 H 0.0732 0.1125 0.8143 117 H 0.0459 0.0400 0.9140