# This file is the result of combining several RDB files, specifically # T0349.t06.dssp-ebghstl.rdb (weight 1.53986) # T0349.t06.stride-ebghtl.rdb (weight 1.24869) # T0349.t06.str2.rdb (weight 1.54758) # T0349.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 T0349.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0349 # 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 T0349.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 5.88375 # # ============================================ # Comments from T0349.t06.stride-ebghtl.rdb # ============================================ # TARGET T0349 # 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 T0349.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 5.88375 # # ============================================ # Comments from T0349.t06.str2.rdb # ============================================ # TARGET T0349 # 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 T0349.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 5.88375 # # ============================================ # Comments from T0349.t06.alpha.rdb # ============================================ # TARGET T0349 # 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 T0349.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 5.88375 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0630 0.2375 0.6995 2 R 0.2194 0.3904 0.3902 3 E 0.3566 0.4341 0.2093 4 L 0.2594 0.5702 0.1704 5 L 0.2568 0.5443 0.1989 6 R 0.1745 0.3970 0.4285 7 T 0.0909 0.3006 0.6085 8 N 0.0316 0.1921 0.7763 9 D 0.0515 0.3636 0.5849 10 A 0.0204 0.8842 0.0954 11 V 0.0087 0.9446 0.0467 12 L 0.0133 0.9460 0.0407 13 L 0.0115 0.9454 0.0431 14 S 0.0203 0.9320 0.0476 15 A 0.0137 0.9371 0.0492 16 V 0.0070 0.9459 0.0471 17 G 0.0067 0.9448 0.0485 18 A 0.0069 0.9328 0.0604 19 L 0.0084 0.9051 0.0865 20 L 0.0233 0.7538 0.2228 21 D 0.0374 0.4466 0.5161 22 G 0.0273 0.2424 0.7303 23 A 0.0387 0.1991 0.7622 24 D 0.0790 0.1380 0.7829 25 I 0.2273 0.0926 0.6801 26 G 0.2303 0.1323 0.6374 27 H 0.6819 0.0894 0.2286 28 L 0.8115 0.0563 0.1321 29 V 0.8293 0.0497 0.1211 30 L 0.7308 0.0509 0.2183 31 D 0.3847 0.0750 0.5403 32 Q 0.0992 0.2379 0.6629 33 N 0.0902 0.1893 0.7206 34 M 0.2038 0.1808 0.6155 35 S 0.3359 0.1951 0.4690 36 I 0.4302 0.2552 0.3146 37 L 0.4397 0.2636 0.2968 38 E 0.3435 0.2592 0.3972 39 G 0.2438 0.1882 0.5681 40 S 0.2810 0.1828 0.5363 41 L 0.3063 0.2118 0.4820 42 G 0.3273 0.1422 0.5306 43 V 0.4325 0.0880 0.4795 44 I 0.4048 0.0421 0.5532 45 P 0.3823 0.0621 0.5556 46 R 0.4461 0.1368 0.4172 47 R 0.6324 0.1288 0.2387 48 V 0.7733 0.0777 0.1489 49 L 0.7599 0.0469 0.1932 50 V 0.6083 0.0336 0.3581 51 H 0.2213 0.0239 0.7548 52 E 0.0145 0.6708 0.3147 53 D 0.0127 0.6853 0.3020 54 D 0.0164 0.7534 0.2303 55 L 0.0072 0.9030 0.0898 56 A 0.0062 0.9280 0.0658 57 G 0.0056 0.9294 0.0650 58 A 0.0048 0.9476 0.0476 59 R 0.0047 0.9557 0.0396 60 R 0.0047 0.9556 0.0397 61 L 0.0048 0.9548 0.0405 62 L 0.0048 0.9528 0.0423 63 T 0.0051 0.9375 0.0574 64 D 0.0058 0.9088 0.0854 65 A 0.0439 0.6291 0.3270 66 G 0.0372 0.0973 0.8655 67 L 0.0700 0.0613 0.8687 68 A 0.1018 0.1280 0.7702 69 H 0.0889 0.4142 0.4969 70 E 0.0983 0.4773 0.4244 71 L 0.1042 0.4384 0.4574 72 R 0.0993 0.2722 0.6285 73 S 0.0584 0.1573 0.7843 74 D 0.0394 0.0963 0.8643 75 D 0.0418 0.0488 0.9095