# This file is the result of combining several RDB files, specifically # T0366.t06.dssp-ebghstl.rdb (weight 1.53986) # T0366.t06.stride-ebghtl.rdb (weight 1.24869) # T0366.t06.str2.rdb (weight 1.54758) # T0366.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 T0366.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0366 # 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 T0366.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 2318 # # ============================================ # Comments from T0366.t06.stride-ebghtl.rdb # ============================================ # TARGET T0366 # 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 T0366.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 2318 # # ============================================ # Comments from T0366.t06.str2.rdb # ============================================ # TARGET T0366 # 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 T0366.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 2318 # # ============================================ # Comments from T0366.t06.alpha.rdb # ============================================ # TARGET T0366 # 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 T0366.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 2318 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.0595 0.0233 0.9172 2 E 0.0572 0.1519 0.7910 3 N 0.0922 0.1594 0.7484 4 L 0.1525 0.2027 0.6448 5 Y 0.2431 0.1861 0.5708 6 F 0.3147 0.1699 0.5153 7 Q 0.2335 0.1522 0.6143 8 S 0.2313 0.1228 0.6459 9 M 0.1607 0.0739 0.7654 10 G 0.1868 0.0251 0.7880 11 L 0.4744 0.0060 0.5196 12 R 0.7690 0.0091 0.2219 13 T 0.9128 0.0032 0.0840 14 V 0.9203 0.0034 0.0763 15 E 0.9191 0.0034 0.0776 16 M 0.8979 0.0036 0.0984 17 K 0.7689 0.0056 0.2255 18 K 0.5644 0.0196 0.4160 19 G 0.1719 0.0164 0.8116 20 P 0.0652 0.0547 0.8802 21 T 0.0505 0.0735 0.8760 22 D 0.0763 0.0944 0.8293 23 S 0.1734 0.0683 0.7583 24 L 0.4966 0.0303 0.4731 25 G 0.7325 0.0127 0.2548 26 I 0.8759 0.0045 0.1196 27 S 0.9029 0.0044 0.0927 28 I 0.8971 0.0047 0.0982 29 A 0.7983 0.0187 0.1829 30 G 0.5210 0.0178 0.4612 31 G 0.2540 0.0285 0.7175 32 V 0.2522 0.0476 0.7002 33 G 0.1701 0.0408 0.7891 34 S 0.1076 0.0406 0.8518 35 P 0.0974 0.0852 0.8173 36 L 0.0721 0.1190 0.8090 37 G 0.0714 0.0755 0.8531 38 D 0.1215 0.0505 0.8280 39 V 0.2712 0.0207 0.7081 40 P 0.5847 0.0089 0.4064 41 I 0.8679 0.0041 0.1279 42 F 0.9082 0.0047 0.0871 43 I 0.9010 0.0043 0.0946 44 A 0.8224 0.0317 0.1459 45 M 0.8379 0.0059 0.1562 46 M 0.7283 0.0092 0.2625 47 H 0.3037 0.0164 0.6799 48 P 0.0665 0.1036 0.8299 49 T 0.0477 0.0788 0.8735 50 G 0.1104 0.1549 0.7348 51 V 0.0530 0.6121 0.3349 52 A 0.0611 0.6766 0.2622 53 A 0.0652 0.6637 0.2712 54 Q 0.0770 0.5789 0.3441 55 T 0.0881 0.2947 0.6171 56 Q 0.0588 0.1748 0.7664 57 K 0.1890 0.0895 0.7216 58 L 0.3381 0.0314 0.6305 59 R 0.1059 0.0232 0.8709 60 V 0.0296 0.1163 0.8541 61 G 0.0365 0.0508 0.9127 62 D 0.2870 0.0333 0.6797 63 R 0.7310 0.0179 0.2510 64 I 0.8828 0.0172 0.1000 65 V 0.8687 0.0183 0.1130 66 T 0.8999 0.0120 0.0880 67 I 0.8271 0.0345 0.1384 68 C 0.3837 0.0645 0.5519 69 G 0.1615 0.0351 0.8035 70 T 0.5828 0.0151 0.4022 71 S 0.5941 0.0163 0.3896 72 T 0.2153 0.1306 0.6541 73 E 0.0610 0.1332 0.8058 74 G 0.0424 0.0723 0.8853 75 M 0.1608 0.0198 0.8194 76 T 0.1629 0.0216 0.8155 77 H 0.0052 0.9313 0.0635 78 T 0.0047 0.9578 0.0375 79 Q 0.0047 0.9595 0.0358 80 A 0.0047 0.9611 0.0342 81 V 0.0047 0.9609 0.0344 82 N 0.0047 0.9597 0.0357 83 L 0.0047 0.9547 0.0406 84 L 0.0057 0.9422 0.0521 85 K 0.0071 0.8777 0.1152 86 N 0.0116 0.6166 0.3717 87 A 0.0655 0.1678 0.7667 88 S 0.0348 0.0697 0.8955 89 G 0.0649 0.0354 0.8997 90 S 0.4701 0.0136 0.5162 91 I 0.8624 0.0038 0.1338 92 E 0.9182 0.0034 0.0785 93 M 0.9289 0.0032 0.0679 94 Q 0.9237 0.0037 0.0726 95 V 0.9152 0.0035 0.0813 96 V 0.7916 0.0079 0.2006 97 A 0.5298 0.0159 0.4543 98 G 0.1265 0.0369 0.8366 99 G 0.0909 0.0397 0.8694 100 D 0.1406 0.0457 0.8138 101 V 0.1678 0.0480 0.7843 102 S 0.1496 0.0530 0.7974 103 E 0.1146 0.0815 0.8040 104 T 0.1395 0.0704 0.7901 105 S 0.1277 0.0504 0.8219 106 V 0.0574 0.0423 0.9004