# This file is the result of combining several RDB files, specifically # T0307.t06.dssp-ebghstl.rdb (weight 1.53986) # T0307.t06.stride-ebghtl.rdb (weight 1.24869) # T0307.t06.str2.rdb (weight 1.54758) # T0307.t06.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 T0307.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0307 # 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 T0307.t06-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 1 # # ============================================ # Comments from T0307.t06.stride-ebghtl.rdb # ============================================ # TARGET T0307 # Using neural net t06-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 T0307.t06-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 1 # # ============================================ # Comments from T0307.t06.str2.rdb # ============================================ # TARGET T0307 # 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 T0307.t06-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 1 # # ============================================ # Comments from T0307.t06.alpha.rdb # ============================================ # TARGET T0307 # Using neural net t06-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 T0307.t06-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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0877 0.1584 0.7540 2 G 0.1069 0.1275 0.7656 3 L 0.1191 0.1545 0.7263 4 G 0.1315 0.1168 0.7517 5 R 0.1651 0.2233 0.6117 6 Q 0.2425 0.1779 0.5795 7 S 0.4002 0.1425 0.4572 8 L 0.4897 0.0933 0.4170 9 N 0.5849 0.0710 0.3441 10 I 0.7116 0.0780 0.2104 11 M 0.7604 0.0566 0.1830 12 T 0.6938 0.0616 0.2447 13 F 0.4592 0.0946 0.4463 14 S 0.1692 0.1062 0.7246 15 G 0.0571 0.1952 0.7477 16 Q 0.1196 0.4806 0.3998 17 E 0.1852 0.5981 0.2167 18 L 0.0903 0.7950 0.1147 19 T 0.0698 0.8481 0.0822 20 A 0.0856 0.8552 0.0592 21 I 0.0811 0.8664 0.0525 22 I 0.0920 0.8505 0.0575 23 K 0.1005 0.8231 0.0763 24 M 0.0819 0.7936 0.1245 25 A 0.0819 0.7310 0.1871 26 K 0.0966 0.6564 0.2470 27 S 0.1820 0.5701 0.2480 28 M 0.2723 0.5081 0.2196 29 V 0.4335 0.3417 0.2248 30 M 0.4215 0.2556 0.3229 31 A 0.2824 0.2231 0.4946 32 D 0.0835 0.0868 0.8297 33 G 0.0711 0.0537 0.8752 34 K 0.2555 0.0295 0.7150 35 I 0.4094 0.0148 0.5758 36 K 0.2091 0.0150 0.7759 37 P 0.2007 0.2658 0.5335 38 A 0.1603 0.4643 0.3754 39 E 0.2491 0.5097 0.2413 40 I 0.4020 0.4196 0.1784 41 A 0.5053 0.3565 0.1381 42 V 0.4990 0.3599 0.1411 43 M 0.4655 0.3039 0.2306 44 T 0.2984 0.3608 0.3409 45 R 0.0586 0.7813 0.1601 46 E 0.0572 0.8089 0.1340 47 F 0.0647 0.8199 0.1154 48 M 0.0970 0.7606 0.1424 49 R 0.1008 0.7425 0.1567 50 F 0.0802 0.6819 0.2379 51 G 0.0983 0.4736 0.4281 52 I 0.1799 0.4577 0.3625 53 L 0.1740 0.4849 0.3411 54 Q 0.0823 0.6076 0.3101 55 D 0.0660 0.6077 0.3262 56 Q 0.0623 0.7309 0.2068 57 V 0.1155 0.7123 0.1722 58 D 0.1365 0.7093 0.1543 59 L 0.1785 0.7159 0.1056 60 L 0.1975 0.6969 0.1056 61 L 0.2326 0.6085 0.1589 62 K 0.1980 0.4993 0.3027 63 A 0.0933 0.4349 0.4718 64 S 0.0561 0.3700 0.5739 65 D 0.0473 0.3112 0.6416 66 S 0.0888 0.4246 0.4866 67 I 0.1322 0.5305 0.3373 68 E 0.1319 0.5035 0.3645 69 A 0.0648 0.6973 0.2379 70 S 0.0524 0.7469 0.2007 71 Q 0.0701 0.7788 0.1511 72 A 0.0929 0.8032 0.1040 73 V 0.1347 0.7838 0.0815 74 A 0.1322 0.7990 0.0688 75 L 0.0954 0.8358 0.0688 76 I 0.1025 0.8013 0.0962 77 A 0.1270 0.6911 0.1819 78 R 0.1122 0.5682 0.3196 79 M 0.0761 0.4074 0.5166 80 D 0.0545 0.3917 0.5538 81 E 0.0057 0.9092 0.0851 82 E 0.0068 0.9115 0.0817 83 R 0.0082 0.9115 0.0803 84 K 0.0116 0.9137 0.0747 85 K 0.0157 0.8972 0.0871 86 Y 0.0266 0.8831 0.0903 87 V 0.0357 0.8687 0.0955 88 A 0.0526 0.8359 0.1115 89 S 0.0708 0.7498 0.1794 90 Y 0.1298 0.6440 0.2261 91 L 0.2433 0.4444 0.3123 92 G 0.4109 0.2585 0.3306 93 V 0.6426 0.1892 0.1681 94 I 0.7551 0.1194 0.1255 95 M 0.7361 0.0790 0.1849 96 A 0.5190 0.0626 0.4184 97 S 0.2536 0.0802 0.6663 98 D 0.1149 0.0619 0.8232 99 G 0.0877 0.0506 0.8616 100 D 0.2000 0.0372 0.7629 101 I 0.2305 0.0726 0.6968 102 D 0.1104 0.0787 0.8109 103 D 0.0342 0.4008 0.5649 104 N 0.0270 0.4832 0.4899 105 E 0.0535 0.7192 0.2273 106 L 0.0771 0.7860 0.1369 107 A 0.0959 0.7985 0.1056 108 L 0.0742 0.8557 0.0701 109 W 0.0775 0.8559 0.0666 110 T 0.0878 0.8493 0.0629 111 L 0.0580 0.8736 0.0684 112 I 0.0441 0.8772 0.0786 113 S 0.0337 0.8653 0.1010 114 T 0.0244 0.8424 0.1332 115 L 0.0344 0.7173 0.2483 116 C 0.0573 0.3829 0.5598 117 G 0.0441 0.1477 0.8083 118 L 0.0691 0.0908 0.8401 119 P 0.0842 0.1744 0.7414 120 T 0.1432 0.3892 0.4676 121 M 0.1860 0.5797 0.2344 122 T 0.1931 0.6527 0.1542 123 V 0.0931 0.8232 0.0837 124 M 0.0610 0.8630 0.0760 125 E 0.0573 0.8651 0.0776 126 A 0.0411 0.8750 0.0840 127 I 0.0313 0.8551 0.1136 128 N 0.0253 0.7647 0.2100 129 N 0.0272 0.6092 0.3635 130 M 0.0413 0.5185 0.4402 131 K 0.0399 0.3938 0.5663 132 N 0.0582 0.1889 0.7529 133 L 0.0375 0.0602 0.9022