# This file is the result of combining several RDB files, specifically # T0381.t06.dssp-ebghstl.rdb (weight 1.53986) # T0381.t06.stride-ebghtl.rdb (weight 1.24869) # T0381.t06.str2.rdb (weight 1.54758) # T0381.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 T0381.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 227.395 # # ============================================ # Comments from T0381.t06.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 227.395 # # ============================================ # Comments from T0381.t06.str2.rdb # ============================================ # TARGET T0381 # 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 T0381.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 227.395 # # ============================================ # Comments from T0381.t06.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 227.395 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0631 0.0201 0.9168 2 T 0.0812 0.0295 0.8893 3 A 0.0541 0.1146 0.8313 4 T 0.0609 0.1053 0.8338 5 E 0.0725 0.0719 0.8556 6 P 0.0657 0.1089 0.8254 7 T 0.0669 0.2678 0.6653 8 E 0.0405 0.4960 0.4635 9 K 0.0453 0.4499 0.5048 10 I 0.0768 0.2476 0.6756 11 L 0.0784 0.0572 0.8645 12 P 0.0560 0.0566 0.8874 13 S 0.0782 0.0279 0.8940 14 P 0.0152 0.4440 0.5408 15 D 0.0184 0.5495 0.4322 16 Y 0.0182 0.7916 0.1901 17 V 0.0146 0.8907 0.0947 18 Q 0.0073 0.9283 0.0643 19 S 0.0065 0.9446 0.0489 20 L 0.0048 0.9543 0.0409 21 A 0.0047 0.9571 0.0382 22 R 0.0048 0.9524 0.0428 23 G 0.0047 0.9568 0.0385 24 L 0.0047 0.9577 0.0376 25 A 0.0047 0.9597 0.0357 26 V 0.0047 0.9591 0.0362 27 I 0.0047 0.9557 0.0396 28 R 0.0049 0.9371 0.0580 29 C 0.0060 0.8983 0.0958 30 F 0.0177 0.7452 0.2371 31 D 0.0384 0.5040 0.4576 32 H 0.0250 0.4887 0.4863 33 R 0.0388 0.3652 0.5961 34 N 0.0432 0.2282 0.7286 35 Q 0.0454 0.1891 0.7655 36 R 0.1024 0.1333 0.7643 37 R 0.1867 0.0563 0.7570 38 T 0.1329 0.0397 0.8274 39 L 0.0048 0.9477 0.0475 40 S 0.0047 0.9598 0.0355 41 D 0.0047 0.9596 0.0358 42 V 0.0047 0.9597 0.0357 43 A 0.0047 0.9583 0.0370 44 R 0.0049 0.9411 0.0541 45 A 0.0058 0.8792 0.1150 46 T 0.0470 0.5136 0.4395 47 D 0.0383 0.0870 0.8747 48 L 0.0563 0.0343 0.9094 49 T 0.0525 0.0648 0.8828 50 R 0.0083 0.8304 0.1613 51 A 0.0068 0.9208 0.0725 52 T 0.0049 0.9456 0.0495 53 A 0.0047 0.9597 0.0356 54 R 0.0047 0.9605 0.0348 55 R 0.0047 0.9605 0.0348 56 F 0.0047 0.9605 0.0349 57 L 0.0047 0.9607 0.0346 58 L 0.0047 0.9596 0.0357 59 T 0.0047 0.9597 0.0356 60 L 0.0047 0.9592 0.0361 61 V 0.0048 0.9517 0.0435 62 E 0.0055 0.9120 0.0825 63 L 0.0430 0.4544 0.5026 64 G 0.0316 0.0508 0.9176 65 Y 0.2027 0.0701 0.7272 66 V 0.7058 0.0310 0.2632 67 A 0.7229 0.0196 0.2575 68 T 0.6908 0.0243 0.2849 69 D 0.2389 0.0323 0.7288 70 G 0.0278 0.0677 0.9045 71 S 0.0757 0.0703 0.8540 72 A 0.4499 0.0468 0.5033 73 F 0.7640 0.0150 0.2210 74 W 0.8016 0.0140 0.1844 75 L 0.5785 0.0260 0.3955 76 T 0.1599 0.0485 0.7915 77 P 0.0086 0.9098 0.0816 78 R 0.0068 0.9410 0.0522 79 V 0.0063 0.9522 0.0415 80 L 0.0085 0.9487 0.0428 81 E 0.0061 0.9448 0.0491 82 L 0.0056 0.9196 0.0748 83 G 0.0068 0.9183 0.0749 84 Y 0.0064 0.9309 0.0627 85 S 0.0064 0.9249 0.0687 86 Y 0.0073 0.8998 0.0929 87 L 0.0124 0.8493 0.1383 88 S 0.0138 0.7050 0.2812 89 S 0.0202 0.4820 0.4978 90 L 0.0600 0.1235 0.8165 91 S 0.0476 0.0471 0.9054