# This file is the result of combining several RDB files, specifically # T0343.t06.dssp-ebghstl.rdb (weight 1.53986) # T0343.t06.stride-ebghtl.rdb (weight 1.24869) # T0343.t06.str2.rdb (weight 1.54758) # T0343.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 T0343.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t06.stride-ebghtl.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t06.str2.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ # Comments from T0343.t06.alpha.rdb # ============================================ # TARGET T0343 # 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 T0343.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 3 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0686 0.0381 0.8933 2 T 0.1169 0.1764 0.7068 3 W 0.0234 0.8503 0.1263 4 R 0.0140 0.9031 0.0829 5 E 0.0132 0.9280 0.0587 6 I 0.0120 0.9243 0.0637 7 L 0.0126 0.9149 0.0724 8 R 0.0166 0.8593 0.1240 9 K 0.0231 0.7969 0.1800 10 E 0.0497 0.3779 0.5725 11 G 0.0449 0.0992 0.8559 12 F 0.2785 0.0675 0.6540 13 L 0.5922 0.0446 0.3633 14 D 0.5635 0.0360 0.4005 15 L 0.2395 0.2690 0.4916 16 G 0.1303 0.1905 0.6792 17 E 0.2372 0.1491 0.6137 18 F 0.7405 0.0298 0.2296 19 I 0.8959 0.0093 0.0948 20 V 0.9206 0.0050 0.0743 21 E 0.9146 0.0069 0.0786 22 L 0.9181 0.0069 0.0750 23 V 0.8945 0.0155 0.0901 24 Y 0.8843 0.0127 0.1030 25 I 0.6974 0.0270 0.2756 26 D 0.3546 0.0390 0.6064 27 C 0.1438 0.0357 0.8205 28 P 0.0867 0.0817 0.8316 29 C 0.1208 0.0668 0.8125 30 E 0.1544 0.0393 0.8063 31 P 0.2009 0.0314 0.7678 32 I 0.1640 0.0166 0.8194 33 P 0.1257 0.0149 0.8594 34 P 0.1771 0.0225 0.8004 35 T 0.5172 0.0232 0.4596 36 L 0.8912 0.0047 0.1041 37 A 0.9236 0.0035 0.0729 38 I 0.9247 0.0037 0.0716 39 Y 0.8906 0.0057 0.1037 40 D 0.5721 0.0120 0.4159 41 K 0.1474 0.0761 0.7765 42 K 0.1072 0.0698 0.8230 43 G 0.0774 0.0577 0.8649 44 D 0.1166 0.0569 0.8265 45 E 0.5504 0.0435 0.4061 46 W 0.8210 0.0241 0.1549 47 Y 0.8670 0.0125 0.1206 48 K 0.8843 0.0111 0.1046 49 V 0.7872 0.0256 0.1873 50 E 0.6095 0.0505 0.3400 51 E 0.4002 0.0367 0.5631 52 A 0.1382 0.0321 0.8297 53 P 0.0809 0.0967 0.8224 54 N 0.0994 0.1005 0.8001 55 V 0.1088 0.2698 0.6214 56 Q 0.0702 0.3913 0.5385 57 N 0.1150 0.4235 0.4615 58 Y 0.0443 0.7496 0.2061 59 R 0.0213 0.8723 0.1064 60 E 0.0156 0.9051 0.0793 61 A 0.0109 0.9173 0.0718 62 V 0.0060 0.9428 0.0512 63 E 0.0047 0.9549 0.0404 64 W 0.0048 0.9521 0.0431 65 A 0.0047 0.9561 0.0392 66 I 0.0047 0.9577 0.0376 67 E 0.0050 0.9581 0.0369 68 V 0.0050 0.9538 0.0413 69 L 0.0056 0.9497 0.0447 70 E 0.0079 0.9418 0.0503 71 R 0.0095 0.9315 0.0590 72 I 0.0217 0.8789 0.0995 73 R 0.0425 0.7379 0.2196 74 D 0.0406 0.3135 0.6459 75 G 0.0327 0.0739 0.8934 76 E 0.0882 0.1070 0.8049 77 N 0.2683 0.0728 0.6589 78 V 0.4491 0.0515 0.4994 79 K 0.5296 0.0519 0.4186 80 L 0.6713 0.0625 0.2662 81 V 0.6613 0.0510 0.2876 82 S 0.5949 0.0431 0.3621 83 L 0.3950 0.0605 0.5445 84 D 0.1527 0.0508 0.7965 85 G 0.0672 0.0388 0.8940 86 P 0.0699 0.0454 0.8846 87 A 0.0825 0.0393 0.8782 88 P 0.0535 0.0622 0.8843 89 P 0.0087 0.8464 0.1449 90 K 0.0067 0.9238 0.0695 91 V 0.0056 0.9451 0.0492 92 M 0.0056 0.9502 0.0443 93 K 0.0050 0.9553 0.0397 94 R 0.0050 0.9522 0.0429 95 L 0.0051 0.9476 0.0473 96 S 0.0053 0.9494 0.0453 97 L 0.0050 0.9451 0.0499 98 A 0.0052 0.9265 0.0683 99 L 0.0053 0.9218 0.0728 100 Q 0.0069 0.8909 0.1023 101 K 0.0090 0.8320 0.1590 102 L 0.0226 0.6760 0.3015 103 T 0.0385 0.3683 0.5933 104 E 0.0239 0.1001 0.8760