PFRMAT SS TARGET T0408 AUTHOR SAM-T06-server METHOD This file is the result of combining several RDB files, specifically METHOD T0408.t04.dssp-ebghstl.rdb (weight 1.53986) METHOD T0408.t04.stride-ebghtl.rdb (weight 1.24869) METHOD T0408.t04.str2.rdb (weight 1.54758) METHOD T0408.t04.alpha.rdb (weight 0.659012) METHOD T0408.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0408.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0408.t2k.str2.rdb (weight 1.54758) METHOD T0408.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 T0408.t04.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0408 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 T0408.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 904 METHOD METHOD ============================================ METHOD Comments from T0408.t04.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0408 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 T0408.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 904 METHOD METHOD ============================================ METHOD Comments from T0408.t04.str2.rdb METHOD ============================================ METHOD TARGET T0408 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 T0408.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 904 METHOD METHOD ============================================ METHOD Comments from T0408.t04.alpha.rdb METHOD ============================================ METHOD TARGET T0408 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 T0408.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 904 METHOD METHOD ============================================ METHOD Comments from T0408.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0408 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 T0408.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 348 METHOD METHOD ============================================ METHOD Comments from T0408.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0408 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 T0408.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 348 METHOD METHOD ============================================ METHOD Comments from T0408.t2k.str2.rdb METHOD ============================================ METHOD TARGET T0408 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 T0408.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 348 METHOD METHOD ============================================ METHOD Comments from T0408.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0408 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 T0408.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 348 METHOD METHOD ============================================ MODEL 1 M C 0.89 K C 0.75 N C 0.69 E C 0.55 V C 0.51 F C 0.48 F C 0.52 G H 0.84 E H 0.91 G H 0.92 M H 0.92 K H 0.91 V H 0.88 V H 0.85 K H 0.81 E H 0.73 K H 0.64 Y C 0.61 P H 0.81 D H 0.88 L H 0.93 Y H 0.95 D H 0.95 I H 0.95 I H 0.95 V H 0.95 K H 0.92 L H 0.87 N H 0.77 D H 0.70 T H 0.70 V H 0.61 F H 0.46 T C 0.66 G C 0.76 K C 0.80 T C 0.79 L C 0.84 D C 0.88 Y H 0.85 K H 0.90 T H 0.94 Q H 0.95 K H 0.96 L H 0.96 I H 0.96 A H 0.96 I H 0.96 G H 0.96 I H 0.96 V H 0.96 A H 0.95 S H 0.92 R H 0.60 C C 0.78 D C 0.85 E H 0.78 V H 0.88 A H 0.93 I H 0.94 E H 0.95 K H 0.96 Q H 0.96 M H 0.96 K H 0.96 S H 0.96 A H 0.96 M H 0.96 K H 0.95 E H 0.86 L C 0.69 G C 0.94 I C 0.93 T C 0.93 K H 0.92 E H 0.94 E H 0.96 I H 0.96 A H 0.96 D H 0.96 V H 0.96 L H 0.96 R H 0.96 V H 0.96 V H 0.96 L H 0.95 L H 0.94 T H 0.88 S H 0.75 G H 0.58 M H 0.74 P H 0.94 A H 0.95 F H 0.96 T H 0.96 K H 0.96 A H 0.96 M H 0.96 K H 0.95 I H 0.94 L H 0.90 E H 0.76 K H 0.55 L C 0.83 END