PFRMAT SS TARGET T0581 AUTHOR SAM-T06-server METHOD This file is the result of combining several RDB files, specifically METHOD T0581.t04.dssp-ebghstl.rdb (weight 1.53986) METHOD T0581.t04.stride-ebghtl.rdb (weight 1.24869) METHOD T0581.t04.str2.rdb (weight 1.54758) METHOD T0581.t04.alpha.rdb (weight 0.659012) METHOD T0581.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0581.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0581.t2k.str2.rdb (weight 1.54758) METHOD T0581.t2k.alpha.rdb (weight 0.659012) 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 T0581.t04.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0581 METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 7 (1 EBGHSTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0581.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 3.21195 METHOD METHOD ============================================ METHOD Comments from T0581.t04.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0581 METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 3 13 METHOD 7 13 METHOD 9 13 METHOD 11 6 (1 EBGHTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0581.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 3.21195 METHOD METHOD ============================================ METHOD Comments from T0581.t04.str2.rdb METHOD ============================================ METHOD TARGET T0581 METHOD Using neural net t04-2621-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 T0581.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 3.21195 METHOD METHOD ============================================ METHOD Comments from T0581.t04.alpha.rdb METHOD ============================================ METHOD TARGET T0581 METHOD Using neural net t04-2621-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 T0581.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 3.21195 METHOD METHOD ============================================ METHOD Comments from T0581.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0581 METHOD Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 7 (1 EBGHSTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0581.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 11 METHOD METHOD ============================================ METHOD Comments from T0581.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0581 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 6 (1 EBGHTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0581.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 11 METHOD METHOD ============================================ METHOD Comments from T0581.t2k.str2.rdb METHOD ============================================ METHOD TARGET T0581 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 13 (1 str2 ) METHOD The input amino acid frequencies were determined from METHOD alignment T0581.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 11 METHOD METHOD ============================================ METHOD Comments from T0581.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0581 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 11 (1 ABCDEFGHIST ) METHOD The input amino acid frequencies were determined from METHOD alignment T0581.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 11 METHOD METHOD ============================================ MODEL 1 M C 0.83 S C 0.56 R H 0.49 F H 0.75 M H 0.87 A H 0.88 L H 0.93 A H 0.93 L H 0.92 C H 0.90 F H 0.80 V H 0.72 L H 0.67 P H 0.86 T H 0.91 A H 0.92 A H 0.91 H H 0.88 A H 0.81 A H 0.67 S H 0.58 L H 0.80 K H 0.86 D H 0.91 F H 0.91 E H 0.91 L H 0.92 S H 0.93 K H 0.94 M H 0.95 L H 0.95 E H 0.95 K H 0.95 V H 0.94 A H 0.93 K H 0.88 E H 0.79 S C 0.52 S C 0.77 V C 0.85 G C 0.88 T C 0.87 P C 0.59 R C 0.46 A H 0.47 I C 0.42 N C 0.55 E C 0.47 D C 0.46 I H 0.65 L H 0.57 D C 0.49 Q C 0.59 G C 0.61 Y C 0.42 T C 0.40 V C 0.41 E C 0.58 G C 0.54 N H 0.53 Q H 0.47 L H 0.46 I H 0.47 N H 0.49 H H 0.44 L C 0.41 S C 0.43 V C 0.57 R C 0.77 A H 0.87 S H 0.91 H H 0.93 A H 0.95 E H 0.95 R H 0.93 M H 0.90 R H 0.87 S H 0.76 N C 0.48 P H 0.92 D H 0.93 S H 0.94 V H 0.95 R H 0.94 S H 0.92 Q H 0.85 L H 0.77 G H 0.78 D H 0.75 S H 0.74 V H 0.71 C H 0.51 S C 0.70 N C 0.65 T H 0.67 G H 0.76 Y H 0.91 R H 0.92 Q H 0.93 L H 0.92 L H 0.85 A H 0.71 R C 0.68 G C 0.83 A C 0.65 I E 0.73 L E 0.86 T E 0.89 Y E 0.87 S E 0.79 F E 0.65 T E 0.54 E E 0.55 Y E 0.47 K C 0.56 T C 0.66 N C 0.76 Q C 0.72 P C 0.53 V C 0.48 A C 0.46 T C 0.43 E H 0.51 R H 0.55 F H 0.46 D H 0.46 A H 0.48 G C 0.59 S C 0.75 C C 0.79 R C 0.72 I C 0.71 Q C 0.74 G C 0.78 K C 0.75 K C 0.90 END