# This file is the result of combining several RDB files, specifically # TR462.t06.str2.rdb (weight 1.54425) # TR462.t06.str4.rdb (weight 0.924988) # TR462.t06.pb.rdb (weight 0.789901) # TR462.t06.bys.rdb (weight 0.748322) # TR462.t06.alpha.rdb (weight 0.678173) # TR462.t04.str2.rdb (weight 1.54425) # TR462.t04.str4.rdb (weight 0.924988) # TR462.t04.pb.rdb (weight 0.789901) # TR462.t04.bys.rdb (weight 0.748322) # TR462.t04.alpha.rdb (weight 0.678173) # TR462.t2k.str2.rdb (weight 1.54425) # TR462.t2k.str4.rdb (weight 0.924988) # TR462.t2k.pb.rdb (weight 0.789901) # TR462.t2k.bys.rdb (weight 0.748322) # TR462.t2k.alpha.rdb (weight 0.678173) # 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 TR462.t06.str2.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-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 TR462.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 75.2253 # # ============================================ # Comments from TR462.t06.str4.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment TR462.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 75.2253 # # ============================================ # Comments from TR462.t06.pb.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment TR462.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 75.2253 # # ============================================ # Comments from TR462.t06.bys.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment TR462.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 75.2253 # # ============================================ # Comments from TR462.t06.alpha.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-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 TR462.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 75.2253 # # ============================================ # Comments from TR462.t04.str2.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-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 TR462.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 68.6508 # # ============================================ # Comments from TR462.t04.str4.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment TR462.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 68.6508 # # ============================================ # Comments from TR462.t04.pb.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment TR462.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 68.6508 # # ============================================ # Comments from TR462.t04.bys.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment TR462.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 68.6508 # # ============================================ # Comments from TR462.t04.alpha.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t04-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 TR462.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 68.6508 # # ============================================ # Comments from TR462.t2k.str2.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-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 TR462.t2k-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 37.5981 # # ============================================ # Comments from TR462.t2k.str4.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment TR462.t2k-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 37.5981 # # ============================================ # Comments from TR462.t2k.pb.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment TR462.t2k-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 37.5981 # # ============================================ # Comments from TR462.t2k.bys.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment TR462.t2k-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 37.5981 # # ============================================ # Comments from TR462.t2k.alpha.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-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 TR462.t2k-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 37.5981 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4954 0.0529 0.4517 2 K 0.4209 0.0523 0.5268 3 L 0.3004 0.3545 0.3452 4 S 0.2007 0.4305 0.3688 5 R 0.3232 0.2178 0.4589 6 L 0.3482 0.0792 0.5726 7 V 0.2523 0.0414 0.7063 8 P 0.1441 0.1260 0.7299 9 G 0.0529 0.1028 0.8442 10 V 0.2686 0.0221 0.7093 11 P 0.5591 0.0175 0.4234 12 A 0.6940 0.0160 0.2900 13 R 0.7845 0.0080 0.2075 14 I 0.7358 0.0089 0.2553 15 K 0.6560 0.0299 0.3141 16 R 0.7011 0.0242 0.2748 17 L 0.5871 0.0432 0.3697 18 E 0.4608 0.0649 0.4743 19 V 0.2688 0.1134 0.6178 20 S 0.1221 0.2104 0.6675 21 G 0.0445 0.4769 0.4786 22 E 0.0353 0.7421 0.2226 23 L 0.0279 0.8438 0.1283 24 H 0.0156 0.8964 0.0880 25 E 0.0120 0.9102 0.0777 26 K 0.0146 0.9042 0.0813 27 L 0.0172 0.8812 0.1015 28 V 0.0211 0.8251 0.1538 29 G 0.0506 0.6462 0.3032 30 M 0.0708 0.2821 0.6471 31 G 0.1251 0.0942 0.7807 32 F 0.2886 0.0479 0.6635 33 V 0.2826 0.0246 0.6928 34 P 0.2145 0.1125 0.6730 35 G 0.1077 0.0970 0.7953 36 E 0.3943 0.0357 0.5700 37 E 0.6886 0.0128 0.2986 38 I 0.7838 0.0076 0.2085 39 E 0.7975 0.0063 0.1962 40 I 0.7874 0.0075 0.2052 41 V 0.7475 0.0197 0.2328 42 Q 0.7318 0.0212 0.2470 43 V 0.6203 0.0495 0.3302 44 A 0.5551 0.0310 0.4139 45 P 0.4198 0.1108 0.4693 46 L 0.1697 0.1493 0.6810 47 G 0.1169 0.1156 0.7674 48 D 0.2331 0.0302 0.7367 49 P 0.3509 0.0483 0.6008 50 I 0.6366 0.0224 0.3410 51 V 0.7957 0.0066 0.1977 52 C 0.8046 0.0060 0.1894 53 K 0.7644 0.0062 0.2293 54 I 0.6641 0.0233 0.3126 55 G 0.4359 0.0444 0.5197 56 N 0.2797 0.0640 0.6564 57 R 0.5042 0.0483 0.4475 58 N 0.6804 0.0281 0.2915 59 I 0.7555 0.0247 0.2198 60 T 0.7423 0.0331 0.2247 61 L 0.6999 0.0586 0.2415 62 R 0.5055 0.1044 0.3901 63 K 0.2374 0.4236 0.3390 64 R 0.1115 0.5453 0.3432 65 E 0.1778 0.4247 0.3974 66 A 0.2697 0.3739 0.3564 67 D 0.3693 0.2534 0.3773 68 L 0.6131 0.0875 0.2994 69 I 0.7148 0.0232 0.2620 70 E 0.7395 0.0123 0.2481 71 V 0.7751 0.0109 0.2140 72 E 0.7318 0.0152 0.2530 73 V 0.6677 0.0201 0.3123 74 V 0.4709 0.0418 0.4873 75 G 0.2644 0.0562 0.6794