PFRMAT SS TARGET T0168 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0168.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0168.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0168.t2k.str.rdb (weight 1.53983) METHOD T0168.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 T0168.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0168 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 T0168.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 36 METHOD METHOD ============================================ METHOD Comments from T0168.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0168 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 T0168.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 36 METHOD METHOD ============================================ METHOD Comments from T0168.t2k.str.rdb METHOD ============================================ METHOD TARGET T0168 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 T0168.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 36 METHOD METHOD ============================================ METHOD Comments from T0168.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0168 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 T0168.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 36 METHOD METHOD ============================================ MODEL 1 M C 0.64 K H 0.68 E H 0.69 L H 0.69 I H 0.65 K H 0.58 E H 0.49 H C 0.50 Q C 0.62 K C 0.69 D C 0.73 I C 0.56 N C 0.50 P H 0.49 A H 0.67 L H 0.75 Q H 0.78 L H 0.90 H H 0.94 D H 0.94 W H 0.94 V H 0.93 E H 0.90 Y H 0.83 Y H 0.72 R H 0.49 P H 0.46 F C 0.50 A C 0.65 A C 0.75 N C 0.83 G C 0.84 Q C 0.65 S C 0.50 A H 0.43 N H 0.50 Y H 0.52 I H 0.44 P H 0.65 A H 0.74 L H 0.79 G H 0.62 K C 0.54 V C 0.78 N C 0.87 D C 0.77 S C 0.78 Q C 0.68 L E 0.52 G E 0.80 I E 0.91 C E 0.92 V E 0.92 L E 0.91 E E 0.62 P C 0.70 D C 0.93 G C 0.89 T E 0.60 M E 0.90 I E 0.84 H E 0.84 A E 0.59 G C 0.68 D C 0.76 W C 0.76 N C 0.80 V C 0.80 S C 0.64 F E 0.51 T E 0.61 M E 0.54 Q C 0.41 S C 0.45 I H 0.40 S H 0.44 K H 0.65 V H 0.92 I H 0.95 S H 0.96 F H 0.96 I H 0.96 A H 0.96 A H 0.95 C H 0.93 M H 0.88 S H 0.77 R H 0.57 G C 0.62 I H 0.80 P H 0.87 Y H 0.91 V H 0.91 L H 0.88 D H 0.85 R H 0.77 V C 0.51 D C 0.84 V C 0.78 E C 0.79 P C 0.82 T C 0.84 G C 0.89 D C 0.83 A C 0.65 F C 0.47 N H 0.48 S H 0.55 I H 0.63 I H 0.61 R H 0.56 L H 0.48 E H 0.45 I H 0.39 N C 0.63 K C 0.80 P C 0.88 G C 0.92 K C 0.88 P C 0.80 F C 0.82 N C 0.84 P C 0.48 M H 0.49 I H 0.53 N H 0.55 A H 0.60 G H 0.58 A H 0.62 L H 0.64 T H 0.66 I H 0.59 A H 0.53 S H 0.45 I C 0.45 L C 0.74 P C 0.85 G C 0.91 E C 0.86 S C 0.85 A H 0.81 Y H 0.89 E H 0.91 K H 0.93 L H 0.95 E H 0.95 F H 0.95 L H 0.96 Y H 0.96 S H 0.96 V H 0.96 M H 0.95 E H 0.95 T H 0.91 L H 0.84 I H 0.49 G C 0.85 K C 0.87 R C 0.78 P C 0.63 R C 0.62 I C 0.57 H C 0.79 E H 0.78 E H 0.84 V H 0.80 F H 0.74 R H 0.64 S H 0.59 E H 0.64 W H 0.59 E H 0.56 T H 0.55 A H 0.62 H H 0.77 R H 0.92 N H 0.94 R H 0.95 A H 0.96 L H 0.96 A H 0.96 Y H 0.96 Y H 0.96 L H 0.95 K H 0.94 E H 0.86 T C 0.58 N C 0.91 F C 0.86 L C 0.78 E C 0.80 A C 0.77 E C 0.70 V H 0.90 E H 0.94 E H 0.95 T H 0.95 L H 0.95 E H 0.95 V H 0.95 Y H 0.94 L H 0.92 K H 0.91 Q H 0.89 C H 0.87 A H 0.85 M H 0.84 E H 0.78 S H 0.63 T H 0.52 T H 0.90 E H 0.94 D H 0.95 I H 0.95 A H 0.96 L H 0.95 I H 0.95 G H 0.95 L H 0.95 I H 0.94 L H 0.91 A H 0.83 H H 0.50 D C 0.81 G C 0.88 Y C 0.74 H C 0.74 P C 0.79 I C 0.77 R C 0.83 H C 0.85 E C 0.69 Q E 0.52 V C 0.54 I C 0.71 P C 0.89 K H 0.81 D H 0.87 V H 0.93 A H 0.95 K H 0.95 L H 0.95 A H 0.95 K H 0.94 A H 0.93 L H 0.92 M H 0.88 L H 0.86 T H 0.81 C H 0.69 G H 0.52 M H 0.56 Y H 0.49 N H 0.56 A H 0.56 S H 0.53 G H 0.57 K H 0.65 Y H 0.69 A H 0.65 A H 0.59 F H 0.54 V C 0.48 G C 0.79 V C 0.82 P C 0.78 A C 0.72 K C 0.73 S C 0.74 G C 0.78 V C 0.76 S C 0.70 G C 0.57 G E 0.80 I E 0.88 M E 0.89 A E 0.90 L E 0.84 V E 0.71 P C 0.68 P C 0.64 S C 0.52 A H 0.55 R H 0.52 R C 0.52 E C 0.57 Q C 0.73 P C 0.72 F C 0.70 Q C 0.74 S C 0.79 G C 0.67 C E 0.57 G E 0.85 I E 0.91 G E 0.91 I E 0.88 Y E 0.71 G C 0.62 P C 0.74 A C 0.73 I C 0.70 D C 0.84 E C 0.78 Y C 0.81 G C 0.80 N C 0.68 S C 0.45 L H 0.83 T H 0.90 G H 0.94 G H 0.96 M H 0.96 L H 0.96 L H 0.96 K H 0.96 H H 0.96 M H 0.95 A H 0.95 Q H 0.92 E H 0.86 W H 0.56 E C 0.86 L C 0.85 S C 0.76 I C 0.73 F C 0.92 END