# This file is the result of combining several RDB files, specifically # T0386.t06.dssp-ebghstl.rdb (weight 1.53986) # T0386.t06.stride-ebghtl.rdb (weight 1.24869) # T0386.t06.str2.rdb (weight 1.54758) # T0386.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 T0386.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.02279 # # ============================================ # Comments from T0386.t06.stride-ebghtl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.02279 # # ============================================ # Comments from T0386.t06.str2.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.02279 # # ============================================ # Comments from T0386.t06.alpha.rdb # ============================================ # TARGET T0386 # 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 T0386.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 3.02279 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0144 0.5121 0.4736 2 L 0.0097 0.8394 0.1509 3 K 0.0051 0.9417 0.0532 4 E 0.0051 0.9452 0.0497 5 F 0.0049 0.9479 0.0472 6 M 0.0048 0.9503 0.0449 7 H 0.0050 0.9430 0.0520 8 T 0.0057 0.9232 0.0711 9 M 0.0083 0.8918 0.0999 10 K 0.0136 0.8161 0.1703 11 N 0.0179 0.6372 0.3450 12 T 0.0477 0.3144 0.6379 13 G 0.0490 0.0886 0.8624 14 R 0.1077 0.0702 0.8222 15 N 0.2147 0.0664 0.7189 16 V 0.1799 0.1961 0.6241 17 N 0.1249 0.1208 0.7543 18 D 0.0936 0.0738 0.8326 19 R 0.2351 0.0177 0.7472 20 P 0.5126 0.0111 0.4763 21 V 0.8478 0.0087 0.1435 22 M 0.9047 0.0087 0.0866 23 V 0.8987 0.0096 0.0916 24 A 0.8139 0.0196 0.1665 25 K 0.6780 0.0309 0.2910 26 E 0.2476 0.0525 0.6999 27 G 0.1163 0.0359 0.8478 28 E 0.4370 0.0240 0.5389 29 T 0.7577 0.0181 0.2242 30 Y 0.7310 0.0200 0.2490 31 T 0.5505 0.0479 0.4016 32 G 0.5245 0.0424 0.4331 33 T 0.6250 0.0543 0.3207 34 Y 0.6379 0.0625 0.2996 35 R 0.4385 0.1118 0.4497 36 G 0.2386 0.0857 0.6757 37 A 0.2226 0.1205 0.6569 38 G 0.2628 0.1116 0.6257 39 L 0.2604 0.1560 0.5836 40 E 0.3169 0.1233 0.5598 41 G 0.6278 0.0652 0.3070 42 F 0.8439 0.0256 0.1305 43 A 0.8870 0.0207 0.0923 44 L 0.8823 0.0170 0.1008 45 N 0.8442 0.0115 0.1443 46 V 0.7534 0.0213 0.2253 47 K 0.3657 0.0495 0.5848 48 G 0.2369 0.0411 0.7220 49 A 0.6381 0.0215 0.3404 50 Y 0.8691 0.0078 0.1231 51 I 0.8915 0.0064 0.1021 52 I 0.7462 0.0302 0.2236 53 G 0.4207 0.0215 0.5579 54 N 0.2979 0.0268 0.6753 55 I 0.0508 0.4942 0.4550 56 D 0.0267 0.4440 0.5293 57 H 0.0286 0.3547 0.6166 58 L 0.1062 0.0226 0.8712 59 P 0.0704 0.0118 0.9179 60 P 0.0180 0.7541 0.2279 61 E 0.0286 0.7516 0.2198 62 Q 0.0442 0.7832 0.1727 63 L 0.2499 0.4577 0.2924 64 K 0.4014 0.2808 0.3177 65 I 0.5469 0.1766 0.2765 66 L 0.4088 0.0693 0.5219 67 K 0.1354 0.0233 0.8413 68 P 0.0313 0.0837 0.8849 69 G 0.0350 0.0415 0.9234 70 D 0.2167 0.0272 0.7561 71 K 0.7030 0.0134 0.2837 72 I 0.8573 0.0061 0.1366 73 T 0.8342 0.0082 0.1576 74 F 0.5966 0.0097 0.3938 75 T 0.1695 0.0156 0.8149