PFRMAT SS TARGET T0142 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0142.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0142.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0142.t2k.str.rdb (weight 1.53983) METHOD T0142.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 T0142.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0142 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 T0142.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 61 METHOD METHOD ============================================ METHOD Comments from T0142.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0142 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 T0142.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 61 METHOD METHOD ============================================ METHOD Comments from T0142.t2k.str.rdb METHOD ============================================ METHOD TARGET T0142 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 T0142.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 61 METHOD METHOD ============================================ METHOD Comments from T0142.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0142 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 T0142.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 61 METHOD METHOD ============================================ MODEL 1 G C 0.80 S C 0.80 P C 0.80 P C 0.69 A C 0.64 Q C 0.49 L E 0.74 S E 0.87 V E 0.93 H E 0.92 T E 0.91 V E 0.88 S E 0.78 W E 0.64 N E 0.50 S C 0.64 G C 0.81 H C 0.84 E C 0.78 R C 0.78 A C 0.84 P C 0.73 T C 0.63 N C 0.54 L H 0.53 E H 0.62 E H 0.69 L H 0.68 L H 0.58 G C 0.55 L C 0.71 N C 0.76 S C 0.72 G C 0.78 E C 0.83 T C 0.81 P C 0.76 D C 0.59 V E 0.86 I E 0.92 A E 0.92 V E 0.88 A E 0.79 V E 0.67 Q E 0.62 G E 0.59 F C 0.47 G C 0.52 F C 0.54 Q C 0.58 T C 0.60 D C 0.54 K C 0.54 P C 0.57 Q C 0.59 Q C 0.63 G C 0.62 P H 0.66 A H 0.77 C H 0.89 V H 0.92 K H 0.93 N H 0.94 F H 0.94 Q H 0.93 S H 0.90 L H 0.82 L C 0.49 T C 0.75 S C 0.80 K C 0.83 G C 0.77 Y E 0.65 T E 0.82 K E 0.85 L E 0.79 K E 0.70 N E 0.59 T E 0.52 I E 0.50 T E 0.54 E E 0.49 T E 0.61 M E 0.71 G E 0.75 L E 0.79 T E 0.81 V E 0.82 Y E 0.82 C E 0.72 L E 0.49 E H 0.57 K H 0.53 H H 0.54 L C 0.57 D C 0.60 Q C 0.50 N C 0.48 T C 0.54 L C 0.59 K C 0.64 N C 0.64 E C 0.52 T C 0.48 I C 0.46 I E 0.46 V C 0.45 T C 0.43 V C 0.47 D C 0.54 D C 0.55 Q C 0.68 K C 0.79 K C 0.79 S C 0.69 G C 0.55 G E 0.71 I E 0.88 V E 0.92 T E 0.92 S E 0.93 F E 0.92 T E 0.91 I E 0.85 Y C 0.54 N C 0.81 K C 0.55 R E 0.80 F E 0.89 S E 0.90 F E 0.91 T E 0.86 T E 0.76 S E 0.50 R C 0.40 M C 0.44 S C 0.55 D C 0.66 E C 0.79 D C 0.59 V C 0.54 T C 0.49 S H 0.67 T H 0.73 N H 0.73 T H 0.77 K H 0.86 Y H 0.88 A H 0.90 Y H 0.95 D H 0.95 T H 0.95 R H 0.95 L H 0.93 D H 0.84 Y H 0.65 S C 0.51 K C 0.64 K C 0.72 D C 0.76 D C 0.81 P C 0.82 S C 0.77 D C 0.62 F E 0.84 L E 0.92 F E 0.92 W E 0.89 I E 0.64 G C 0.53 D C 0.65 L C 0.61 N C 0.51 V C 0.45 R E 0.51 V C 0.53 E C 0.74 T C 0.80 N C 0.77 A H 0.65 T H 0.83 H H 0.88 A H 0.91 K H 0.92 S H 0.92 L H 0.91 V H 0.87 D H 0.79 Q H 0.61 N C 0.62 N C 0.66 I H 0.81 D H 0.86 G H 0.86 L H 0.83 M H 0.81 A H 0.84 F H 0.83 D H 0.80 Q H 0.86 L H 0.88 K H 0.89 K H 0.84 A H 0.80 K H 0.71 E C 0.55 Q C 0.78 K C 0.76 L C 0.63 F C 0.65 D C 0.67 G C 0.68 W C 0.58 T C 0.51 E C 0.53 P C 0.64 Q C 0.65 V C 0.68 T C 0.71 F C 0.73 K C 0.85 P C 0.84 T C 0.66 Y C 0.51 K E 0.49 F C 0.52 K C 0.69 P C 0.83 N C 0.88 T C 0.83 D C 0.78 E C 0.76 Y C 0.75 D C 0.76 L C 0.80 S C 0.77 A C 0.63 T C 0.68 P C 0.67 S C 0.57 W C 0.47 T C 0.46 D E 0.45 R E 0.66 A E 0.72 L E 0.74 Y E 0.72 K C 0.49 S C 0.76 G C 0.84 T C 0.82 G C 0.74 K C 0.62 T C 0.51 I E 0.52 Q E 0.60 P E 0.62 L E 0.56 S E 0.52 Y C 0.43 N C 0.51 S C 0.61 L C 0.66 T C 0.70 N C 0.62 Y C 0.53 K E 0.53 Q C 0.54 T C 0.71 E C 0.76 H C 0.76 R C 0.75 P C 0.56 V E 0.72 L E 0.86 A E 0.90 K E 0.91 F E 0.90 R E 0.88 V E 0.80 T E 0.63 L C 0.89 END