# This file is the result of combining several RDB files, specifically # T0564.t04.dssp-ebghstl.rdb (weight 1.53986) # T0564.t04.stride-ebghtl.rdb (weight 1.24869) # T0564.t04.str2.rdb (weight 1.54758) # T0564.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 T0564.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0564 # 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 T0564.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 38.4637 # # ============================================ # Comments from T0564.t04.stride-ebghtl.rdb # ============================================ # TARGET T0564 # 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 T0564.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 38.4637 # # ============================================ # Comments from T0564.t04.str2.rdb # ============================================ # TARGET T0564 # 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 T0564.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 38.4637 # # ============================================ # Comments from T0564.t04.alpha.rdb # ============================================ # TARGET T0564 # 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 T0564.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 38.4637 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0654 0.0337 0.9009 2 A 0.1157 0.0137 0.8706 3 P 0.1855 0.0272 0.7873 4 L 0.4227 0.0375 0.5397 5 Q 0.6140 0.0256 0.3604 6 Q 0.7777 0.0143 0.2081 7 K 0.8384 0.0073 0.1543 8 Q 0.8777 0.0040 0.1183 9 V 0.8879 0.0039 0.1082 10 V 0.9153 0.0043 0.0804 11 V 0.9108 0.0035 0.0857 12 S 0.8135 0.0247 0.1618 13 N 0.7113 0.0126 0.2760 14 K 0.5259 0.0702 0.4039 15 R 0.4404 0.0615 0.4980 16 E 0.4105 0.0525 0.5370 17 K 0.2762 0.0201 0.7037 18 P 0.2036 0.0324 0.7641 19 V 0.1801 0.0776 0.7423 20 N 0.1163 0.1116 0.7721 21 D 0.0982 0.1168 0.7849 22 R 0.1157 0.1956 0.6887 23 R 0.1737 0.1765 0.6498 24 S 0.1465 0.1939 0.6596 25 R 0.1083 0.1815 0.7102 26 Q 0.1362 0.2178 0.6460 27 Q 0.1626 0.1862 0.6513 28 E 0.2667 0.1399 0.5934 29 V 0.4327 0.0920 0.4754 30 S 0.3460 0.0469 0.6071 31 P 0.2278 0.0601 0.7121 32 A 0.1270 0.0853 0.7877 33 G 0.0970 0.0646 0.8384 34 T 0.1494 0.0661 0.7845 35 S 0.2963 0.0258 0.6780 36 M 0.6798 0.0080 0.3122 37 R 0.8678 0.0043 0.1279 38 Y 0.9177 0.0037 0.0786 39 E 0.9279 0.0033 0.0688 40 A 0.9221 0.0034 0.0745 41 S 0.9152 0.0039 0.0810 42 F 0.8899 0.0063 0.1038 43 K 0.8399 0.0067 0.1534 44 P 0.7777 0.0060 0.2163 45 L 0.3198 0.0406 0.6395 46 N 0.1584 0.0386 0.8030 47 G 0.0747 0.0513 0.8740 48 G 0.1020 0.0367 0.8613 49 L 0.4071 0.0413 0.5517 50 E 0.7613 0.0205 0.2183 51 K 0.8090 0.0101 0.1809 52 T 0.8898 0.0060 0.1042 53 F 0.9048 0.0048 0.0904 54 R 0.8839 0.0059 0.1102 55 L 0.7492 0.0079 0.2429 56 Q 0.4267 0.0153 0.5580 57 A 0.0958 0.5528 0.3514 58 Q 0.1065 0.6303 0.2632 59 Q 0.1534 0.6024 0.2442 60 Y 0.1987 0.5351 0.2662 61 H 0.1902 0.4185 0.3913 62 A 0.2582 0.2816 0.4603 63 L 0.3308 0.0856 0.5836 64 T 0.2821 0.0651 0.6528 65 V 0.1393 0.1753 0.6854 66 G 0.0854 0.0994 0.8152 67 D 0.2626 0.1111 0.6263 68 Q 0.4420 0.0469 0.5111 69 G 0.6481 0.0178 0.3340 70 T 0.8438 0.0093 0.1469 71 L 0.8949 0.0049 0.1002 72 S 0.8807 0.0089 0.1103 73 Y 0.8549 0.0094 0.1357 74 K 0.6853 0.0303 0.2844 75 G 0.4374 0.0327 0.5299 76 T 0.6380 0.0361 0.3259 77 R 0.8035 0.0195 0.1770 78 F 0.8570 0.0174 0.1256 79 V 0.8019 0.0354 0.1627 80 G 0.7974 0.0240 0.1786 81 F 0.7694 0.0312 0.1994 82 V 0.6832 0.0327 0.2841 83 S 0.4944 0.0433 0.4623 84 R 0.2591 0.0548 0.6860 85 T 0.1346 0.0244 0.8410 86 P 0.0808 0.0837 0.8355 87 D 0.0626 0.1162 0.8212 88 N 0.0627 0.0793 0.8580 89 E 0.0582 0.0892 0.8526