PFRMAT SS TARGET T0557 AUTHOR SAM-T08-server METHOD This file is the result of combining several RDB files, specifically METHOD T0557.t06.str2.rdb (weight 1.54425) METHOD T0557.t06.str4.rdb (weight 0.924988) METHOD T0557.t06.pb.rdb (weight 0.789901) METHOD T0557.t06.bys.rdb (weight 0.748322) METHOD T0557.t06.alpha.rdb (weight 0.678173) METHOD T0557.t04.str2.rdb (weight 1.54425) METHOD T0557.t04.str4.rdb (weight 0.924988) METHOD T0557.t04.pb.rdb (weight 0.789901) METHOD T0557.t04.bys.rdb (weight 0.748322) METHOD T0557.t04.alpha.rdb (weight 0.678173) METHOD T0557.t2k.str2.rdb (weight 1.54425) METHOD T0557.t2k.str4.rdb (weight 0.924988) METHOD T0557.t2k.pb.rdb (weight 0.789901) METHOD T0557.t2k.bys.rdb (weight 0.748322) METHOD T0557.t2k.alpha.rdb (weight 0.678173) METHOD These files were combined by translating their predictions into EHL METHOD predictions with tables generated by compare-real, and then combining METHOD those predictions with weights proportional to their mutual information METHOD with the EHL alphabet. The comments from the individual files follow. METHOD METHOD Comments from T0557.t06.str2.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 13 (1 str2 ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t06-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 904 METHOD METHOD ============================================ METHOD Comments from T0557.t06.str4.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 21 (1 str4 ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t06-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 904 METHOD METHOD ============================================ METHOD Comments from T0557.t06.pb.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 16 (1 pb ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t06-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 904 METHOD METHOD ============================================ METHOD Comments from T0557.t06.bys.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 11 (1 Bystroff ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t06-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 904 METHOD METHOD ============================================ METHOD Comments from T0557.t06.alpha.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 11 (1 ABCDEFGHIST ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t06-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 904 METHOD METHOD ============================================ METHOD Comments from T0557.t04.str2.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 13 (1 str2 ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t04-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 874 METHOD METHOD ============================================ METHOD Comments from T0557.t04.str4.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 21 (1 str4 ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t04-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 874 METHOD METHOD ============================================ METHOD Comments from T0557.t04.pb.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 16 (1 pb ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t04-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 874 METHOD METHOD ============================================ METHOD Comments from T0557.t04.bys.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 11 (1 Bystroff ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t04-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 874 METHOD METHOD ============================================ METHOD Comments from T0557.t04.alpha.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 11 (1 ABCDEFGHIST ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t04-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 874 METHOD METHOD ============================================ METHOD Comments from T0557.t2k.str2.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 13 (1 str2 ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 113.814 METHOD METHOD ============================================ METHOD Comments from T0557.t2k.str4.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 21 (1 str4 ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 113.814 METHOD METHOD ============================================ METHOD Comments from T0557.t2k.pb.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 16 (1 pb ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 113.814 METHOD METHOD ============================================ METHOD Comments from T0557.t2k.bys.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 11 (1 Bystroff ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 113.814 METHOD METHOD ============================================ METHOD Comments from T0557.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0557 METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 11 (1 ABCDEFGHIST ) METHOD The input amino acid frequencies were determined from METHOD alignment T0557.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 113.814 METHOD METHOD ============================================ MODEL 1 M C 0.51 R C 0.43 S H 0.61 A H 0.76 T H 0.86 D H 0.90 L H 0.91 L H 0.91 D H 0.91 E H 0.90 L H 0.83 N H 0.72 A H 0.56 V H 0.46 D H 0.52 E H 0.59 S H 0.60 A H 0.65 R H 0.73 I H 0.79 E H 0.81 A H 0.84 K H 0.81 R H 0.68 A H 0.52 S C 0.54 D C 0.63 M C 0.70 G C 0.63 K H 0.58 S H 0.54 V H 0.64 M H 0.68 E H 0.70 T H 0.62 V H 0.60 I H 0.55 A H 0.56 F H 0.39 A C 0.45 N C 0.63 E C 0.69 P C 0.69 G C 0.78 L C 0.67 D C 0.70 G C 0.67 G E 0.53 Y E 0.77 L E 0.80 L E 0.80 L E 0.75 G E 0.65 V E 0.60 D E 0.48 W C 0.42 A C 0.48 I C 0.61 N C 0.71 D C 0.62 K C 0.62 G C 0.60 D C 0.56 T C 0.47 V E 0.50 Y E 0.49 R C 0.64 P C 0.53 V C 0.69 G C 0.81 L C 0.77 P C 0.72 D C 0.79 P H 0.67 D H 0.84 K H 0.90 V H 0.91 Q H 0.91 R H 0.91 D H 0.89 L H 0.85 A H 0.82 S H 0.78 Q H 0.78 C H 0.74 A H 0.72 S H 0.61 M C 0.47 L C 0.57 N C 0.64 V C 0.60 A C 0.61 L C 0.59 R C 0.71 P C 0.61 E C 0.60 M E 0.58 Q E 0.67 L E 0.74 E E 0.72 Q E 0.66 V E 0.51 G C 0.70 G C 0.81 K C 0.59 T E 0.65 L E 0.80 L E 0.82 V E 0.82 V E 0.82 Y E 0.79 V E 0.50 P C 0.67 E C 0.61 A C 0.60 D C 0.72 V C 0.51 T C 0.56 H C 0.64 K C 0.65 P C 0.56 I E 0.63 Y E 0.71 K E 0.66 K E 0.51 A C 0.50 T C 0.73 G C 0.80 L C 0.73 P C 0.65 G C 0.71 G C 0.64 A E 0.57 Y E 0.73 R E 0.75 R E 0.67 I C 0.51 G C 0.71 S C 0.67 S C 0.62 D C 0.55 Q C 0.48 R C 0.49 C C 0.55 V C 0.68 END