PFRMAT SS TARGET T0157 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0157.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0157.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0157.t2k.str.rdb (weight 1.53983) METHOD T0157.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 T0157.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0157 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 T0157.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 56 METHOD METHOD ============================================ METHOD Comments from T0157.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0157 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 T0157.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 56 METHOD METHOD ============================================ METHOD Comments from T0157.t2k.str.rdb METHOD ============================================ METHOD TARGET T0157 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.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 str ) METHOD The input amino acid frequencies were determined from METHOD alignment T0157.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 56 METHOD METHOD ============================================ METHOD Comments from T0157.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0157 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 T0157.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 56 METHOD METHOD ============================================ MODEL 1 M C 0.89 S C 0.84 G C 0.68 T E 0.69 L E 0.87 L E 0.89 A E 0.90 F E 0.86 D E 0.59 F C 0.75 G C 0.86 T C 0.76 K C 0.51 S E 0.78 I E 0.84 G E 0.85 V E 0.90 A E 0.88 V E 0.81 G E 0.56 Q C 0.76 R C 0.68 I C 0.67 T C 0.65 G C 0.63 T C 0.50 A E 0.44 R C 0.48 P C 0.50 L C 0.40 P E 0.40 A E 0.54 I E 0.65 K E 0.61 A C 0.48 Q C 0.68 D C 0.81 G C 0.82 T C 0.69 P H 0.53 D H 0.60 W H 0.93 N H 0.95 I H 0.95 I H 0.96 E H 0.96 R H 0.95 L H 0.95 L H 0.94 K H 0.92 E H 0.76 W C 0.49 Q C 0.86 P C 0.83 D C 0.59 E E 0.89 I E 0.93 I E 0.92 V E 0.85 G E 0.60 L C 0.68 P C 0.68 L C 0.48 N C 0.81 M C 0.86 D C 0.91 G C 0.93 T C 0.85 E C 0.65 Q C 0.73 P H 0.60 L H 0.84 T H 0.93 A H 0.95 R H 0.95 A H 0.96 R H 0.96 K H 0.96 F H 0.96 A H 0.96 N H 0.96 R H 0.95 I H 0.94 H H 0.90 G H 0.79 R H 0.64 F C 0.66 G C 0.92 V C 0.88 E C 0.57 V E 0.86 K E 0.91 L E 0.88 H E 0.76 D C 0.51 E C 0.75 R C 0.72 L C 0.61 S C 0.53 T H 0.80 V H 0.94 E H 0.96 A H 0.96 R H 0.96 S H 0.95 G H 0.95 L H 0.94 F H 0.93 E H 0.87 Q C 0.60 G C 0.93 G C 0.88 Y C 0.79 R H 0.57 A H 0.66 L H 0.65 N H 0.57 K H 0.50 G C 0.51 K H 0.57 V H 0.71 D H 0.82 S H 0.95 A H 0.96 S H 0.96 A H 0.96 V H 0.96 I H 0.96 I H 0.96 L H 0.95 E H 0.94 S H 0.92 Y H 0.90 F H 0.84 E H 0.70 Q C 0.57 G C 0.81 Y C 0.92 END