# This file is the result of combining several RDB files, specifically # T0201.t04.dssp-ebghstl.rdb (weight 1.53986) # T0201.t04.stride-ebghtl.rdb (weight 1.24869) # T0201.t04.str2.rdb (weight 1.54758) # T0201.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 T0201.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0201 # 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 T0201.t04-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 35 # # ============================================ # Comments from T0201.t04.stride-ebghtl.rdb # ============================================ # TARGET T0201 # 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 T0201.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 25.3946 # # ============================================ # Comments from T0201.t04.str2.rdb # ============================================ # TARGET T0201 # 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 T0201.t04-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 35 # # ============================================ # Comments from T0201.t04.alpha.rdb # ============================================ # TARGET T0201 # 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 T0201.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 25.3946 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1817 0.0096 0.8087 2 I 0.5423 0.0058 0.4519 3 K 0.7391 0.0051 0.2558 4 V 0.7802 0.0054 0.2144 5 T 0.5766 0.0070 0.4164 6 V 0.3077 0.0415 0.6508 7 T 0.1141 0.0396 0.8463 8 N 0.1087 0.0398 0.8515 9 S 0.2936 0.0198 0.6866 10 F 0.7887 0.0048 0.2065 11 F 0.8789 0.0045 0.1166 12 E 0.8949 0.0040 0.1011 13 V 0.8451 0.0044 0.1505 14 T 0.6307 0.0247 0.3446 15 G 0.3467 0.0224 0.6308 16 H 0.2018 0.0315 0.7667 17 A 0.1338 0.0455 0.8207 18 P 0.0781 0.0928 0.8291 19 D 0.0356 0.2117 0.7527 20 K 0.0848 0.3035 0.6117 21 T 0.2175 0.4503 0.3322 22 L 0.2123 0.5727 0.2150 23 C 0.1147 0.7571 0.1282 24 A 0.0514 0.8405 0.1081 25 S 0.0302 0.8962 0.0737 26 V 0.0117 0.9303 0.0580 27 S 0.0071 0.9509 0.0420 28 L 0.0055 0.9563 0.0382 29 L 0.0048 0.9583 0.0368 30 T 0.0048 0.9574 0.0379 31 Q 0.0048 0.9570 0.0382 32 H 0.0051 0.9551 0.0398 33 V 0.0049 0.9511 0.0440 34 A 0.0051 0.9516 0.0434 35 N 0.0055 0.9461 0.0484 36 F 0.0060 0.9383 0.0557 37 L 0.0078 0.9295 0.0627 38 K 0.0104 0.9022 0.0874 39 A 0.0114 0.8401 0.1485 40 E 0.0252 0.6964 0.2784 41 K 0.0499 0.3863 0.5638 42 K 0.0679 0.1660 0.7661 43 A 0.2207 0.0742 0.7051 44 K 0.4456 0.0305 0.5239 45 I 0.5471 0.0219 0.4310 46 K 0.6422 0.0258 0.3320 47 K 0.4903 0.0452 0.4645 48 E 0.2707 0.0787 0.6507 49 S 0.0952 0.0374 0.8674 50 G 0.2135 0.0233 0.7632 51 Y 0.7506 0.0065 0.2429 52 L 0.9069 0.0036 0.0895 53 K 0.9206 0.0036 0.0759 54 V 0.9099 0.0041 0.0860 55 K 0.8780 0.0043 0.1176 56 F 0.6428 0.0229 0.3344 57 E 0.1621 0.1083 0.7296 58 E 0.0884 0.0866 0.8250 59 L 0.0750 0.0806 0.8444 60 E 0.0461 0.1247 0.8292 61 N 0.0353 0.6419 0.3228 62 C 0.0331 0.7793 0.1877 63 E 0.0184 0.9142 0.0674 64 V 0.0137 0.9407 0.0456 65 K 0.0080 0.9513 0.0407 66 V 0.0056 0.9568 0.0376 67 L 0.0047 0.9599 0.0354 68 A 0.0047 0.9596 0.0358 69 A 0.0047 0.9588 0.0366 70 M 0.0047 0.9591 0.0362 71 V 0.0047 0.9594 0.0359 72 R 0.0047 0.9539 0.0414 73 S 0.0048 0.9428 0.0524 74 L 0.0047 0.9532 0.0421 75 K 0.0047 0.9547 0.0406 76 E 0.0047 0.9473 0.0480 77 L 0.0048 0.9364 0.0588 78 E 0.0054 0.9193 0.0753 79 Q 0.0061 0.8336 0.1604 80 K 0.0179 0.6437 0.3384 81 F 0.0957 0.1447 0.7596 82 P 0.0197 0.3161 0.6642 83 S 0.0211 0.2603 0.7186 84 Q 0.2129 0.1986 0.5885 85 I 0.7018 0.0105 0.2876 86 R 0.8717 0.0059 0.1224 87 V 0.8953 0.0054 0.0993 88 E 0.8655 0.0089 0.1256 89 V 0.8515 0.0091 0.1393 90 I 0.7086 0.0229 0.2685 91 D 0.5037 0.0391 0.4572 92 N 0.2359 0.0545 0.7096 93 G 0.0910 0.0373 0.8717 94 S 0.0597 0.0241 0.9162