PFRMAT SS TARGET T0182 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0182.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0182.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0182.t2k.str.rdb (weight 1.53983) METHOD T0182.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 T0182.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0182 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 T0182.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 300 METHOD METHOD ============================================ METHOD Comments from T0182.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0182 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 T0182.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 300 METHOD METHOD ============================================ METHOD Comments from T0182.t2k.str.rdb METHOD ============================================ METHOD TARGET T0182 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 T0182.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 300 METHOD METHOD ============================================ METHOD Comments from T0182.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0182 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 T0182.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 300 METHOD METHOD ============================================ MODEL 1 M C 0.89 I C 0.62 R C 0.56 I C 0.73 K C 0.87 T C 0.93 P H 0.92 S H 0.95 E H 0.95 I H 0.96 E H 0.96 K H 0.96 M H 0.96 K H 0.96 K H 0.96 A H 0.95 G H 0.96 K H 0.96 A H 0.96 V H 0.96 A H 0.96 V H 0.96 A H 0.96 L H 0.96 R H 0.95 E H 0.94 V H 0.93 R H 0.92 K H 0.86 V H 0.76 I H 0.48 V C 0.77 P C 0.87 G C 0.94 K C 0.83 T C 0.79 A H 0.93 W H 0.95 D H 0.96 V H 0.96 E H 0.96 T H 0.96 L H 0.96 V H 0.96 L H 0.95 E H 0.95 I H 0.95 F H 0.95 K H 0.94 K H 0.88 L H 0.52 R C 0.82 V C 0.83 K C 0.73 P C 0.68 A C 0.67 F C 0.66 K C 0.67 G C 0.72 Y C 0.74 G C 0.74 G C 0.74 Y C 0.73 K C 0.69 Y C 0.54 A E 0.60 T E 0.68 C E 0.64 V C 0.51 S C 0.72 V C 0.67 N C 0.68 E C 0.61 E C 0.54 V C 0.52 V C 0.55 H C 0.65 G C 0.73 L C 0.78 P C 0.82 L C 0.83 K C 0.84 E C 0.77 K C 0.61 V E 0.58 F C 0.56 K C 0.79 E C 0.88 G C 0.93 D C 0.73 I E 0.82 V E 0.90 S E 0.92 V E 0.89 D E 0.76 V E 0.66 G E 0.56 A E 0.68 V E 0.70 Y E 0.61 Q C 0.80 G C 0.82 L E 0.48 Y E 0.62 G E 0.56 D E 0.49 A E 0.56 A E 0.63 V E 0.67 T E 0.73 Y E 0.72 I E 0.62 V C 0.64 G C 0.84 E C 0.89 T C 0.91 D C 0.93 E H 0.91 R H 0.94 G H 0.95 K H 0.96 E H 0.96 L H 0.96 V H 0.96 R H 0.96 V H 0.96 T H 0.96 R H 0.96 E H 0.96 V H 0.96 L H 0.96 E H 0.95 K H 0.95 A H 0.95 I H 0.93 K H 0.86 M H 0.69 I C 0.54 K C 0.83 P C 0.85 G C 0.92 I C 0.80 R C 0.73 L H 0.70 G H 0.79 D H 0.83 V H 0.93 S H 0.95 H H 0.96 C H 0.96 I H 0.96 Q H 0.96 E H 0.96 T H 0.96 V H 0.95 E H 0.94 S H 0.87 V C 0.52 G C 0.92 F C 0.90 N C 0.79 V C 0.62 I C 0.58 R C 0.56 D C 0.63 Y C 0.61 V C 0.61 G C 0.62 H C 0.62 G C 0.61 V C 0.59 G C 0.63 R C 0.51 E E 0.48 L C 0.44 H C 0.60 E C 0.72 D C 0.78 P C 0.75 Q C 0.63 I C 0.53 P C 0.55 N C 0.58 Y C 0.63 G C 0.73 T C 0.81 P C 0.79 G C 0.82 T C 0.81 G C 0.73 V C 0.63 V E 0.56 L E 0.54 R C 0.73 K C 0.89 G C 0.92 M C 0.60 T E 0.84 L E 0.89 A E 0.88 I E 0.83 E E 0.66 P E 0.57 M E 0.63 V E 0.67 S E 0.62 E C 0.54 G C 0.74 D C 0.77 W C 0.74 R C 0.57 V E 0.55 V E 0.59 V E 0.55 K C 0.64 E C 0.75 D C 0.82 G C 0.75 W C 0.53 T E 0.68 A E 0.76 V E 0.74 T E 0.60 V C 0.57 D C 0.80 G C 0.83 S C 0.57 R E 0.70 C E 0.82 A E 0.90 H E 0.91 F E 0.90 E E 0.84 H E 0.79 T E 0.86 I E 0.92 L E 0.92 I E 0.89 T E 0.60 E C 0.82 N C 0.91 G C 0.84 A C 0.54 E E 0.77 I E 0.80 L E 0.61 T C 0.59 K C 0.75 E C 0.87 G C 0.92 END