# This file is the result of combining several RDB files, specifically # T0472.t06.str2.rdb (weight 1.54425) # T0472.t06.str4.rdb (weight 0.924988) # T0472.t06.pb.rdb (weight 0.789901) # T0472.t06.bys.rdb (weight 0.748322) # T0472.t06.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 T0472.t06.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ # Comments from T0472.t06.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ # Comments from T0472.t06.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ # Comments from T0472.t06.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ # Comments from T0472.t06.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2622 0.1498 0.5880 2 S 0.2606 0.1543 0.5851 3 G 0.3472 0.1612 0.4916 4 W 0.5248 0.1237 0.3515 5 Y 0.6926 0.0537 0.2537 6 E 0.7238 0.0391 0.2370 7 L 0.7240 0.0335 0.2425 8 S 0.6654 0.0449 0.2898 9 K 0.5615 0.0959 0.3426 10 S 0.3518 0.1238 0.5243 11 S 0.1557 0.2429 0.6014 12 N 0.1229 0.1379 0.7392 13 D 0.1361 0.0860 0.7779 14 Q 0.4626 0.0316 0.5058 15 F 0.7011 0.0126 0.2863 16 K 0.7894 0.0081 0.2025 17 F 0.8243 0.0045 0.1711 18 V 0.8079 0.0055 0.1866 19 L 0.7922 0.0078 0.2000 20 K 0.7796 0.0126 0.2078 21 A 0.6357 0.0354 0.3289 22 G 0.3018 0.1248 0.5733 23 N 0.1361 0.1062 0.7576 24 G 0.1380 0.0717 0.7903 25 E 0.4924 0.0323 0.4752 26 V 0.7084 0.0185 0.2731 27 I 0.7130 0.0294 0.2576 28 L 0.7144 0.0354 0.2502 29 T 0.6173 0.0657 0.3170 30 S 0.4460 0.0881 0.4659 31 E 0.2788 0.2586 0.4626 32 L 0.2544 0.3122 0.4334 33 Y 0.2703 0.2624 0.4672 34 T 0.2421 0.2228 0.5351 35 G 0.1651 0.2276 0.6074 36 K 0.0543 0.6258 0.3199 37 S 0.0595 0.6589 0.2815 38 G 0.0532 0.6804 0.2663 39 A 0.0403 0.7843 0.1753 40 M 0.0361 0.7480 0.2159 41 N 0.0479 0.6359 0.3162 42 G 0.0708 0.6367 0.2925 43 I 0.0692 0.7125 0.2184 44 E 0.0588 0.7507 0.1904 45 S 0.0783 0.7350 0.1867 46 V 0.1205 0.6385 0.2410 47 Q 0.1305 0.5425 0.3270 48 T 0.1252 0.4040 0.4708 49 N 0.1008 0.1811 0.7180 50 S 0.1895 0.0808 0.7297 51 P 0.1353 0.1929 0.6718 52 I 0.1363 0.2889 0.5748 53 E 0.1565 0.2594 0.5841 54 A 0.1808 0.1967 0.6225 55 R 0.1975 0.1426 0.6599