PFRMAT SS TARGET T0173 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0173.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0173.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0173.t2k.str.rdb (weight 1.53983) METHOD T0173.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 T0173.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0173 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 T0173.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 64 METHOD METHOD ============================================ METHOD Comments from T0173.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0173 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 T0173.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 64 METHOD METHOD ============================================ METHOD Comments from T0173.t2k.str.rdb METHOD ============================================ METHOD TARGET T0173 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 T0173.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 64 METHOD METHOD ============================================ METHOD Comments from T0173.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0173 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 T0173.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 64 METHOD METHOD ============================================ MODEL 1 M C 0.91 S C 0.89 E C 0.85 T C 0.80 P C 0.78 R E 0.71 L E 0.91 L E 0.92 F E 0.93 V E 0.88 H E 0.75 A C 0.59 H C 0.84 P C 0.80 D C 0.78 D H 0.53 E H 0.74 S H 0.77 L H 0.71 S H 0.65 N H 0.76 G H 0.90 A H 0.95 T H 0.96 I H 0.96 A H 0.96 H H 0.96 Y H 0.96 T H 0.95 S H 0.90 R C 0.61 G C 0.95 A C 0.92 Q E 0.55 V E 0.89 H E 0.93 V E 0.93 V E 0.93 T E 0.92 C E 0.75 T C 0.54 L C 0.76 G C 0.82 E C 0.73 E C 0.75 G C 0.78 E C 0.75 V C 0.67 I C 0.72 G C 0.77 D H 0.49 R H 0.57 W H 0.53 A C 0.48 Q C 0.62 L C 0.75 T C 0.76 A C 0.75 D C 0.76 H C 0.82 A H 0.65 D H 0.62 Q H 0.64 L H 0.65 G H 0.79 G H 0.87 Y H 0.88 R H 0.89 I H 0.95 G H 0.95 E H 0.95 L H 0.96 T H 0.96 A H 0.96 A H 0.96 L H 0.96 R H 0.95 A H 0.91 L C 0.55 G C 0.93 V C 0.90 S C 0.85 A C 0.63 P C 0.45 I E 0.46 Y E 0.53 L C 0.57 G C 0.74 G C 0.70 A C 0.65 G C 0.68 R C 0.68 W C 0.75 R C 0.75 D C 0.74 S C 0.71 G C 0.65 M C 0.56 A C 0.52 G C 0.60 T C 0.70 D C 0.75 Q C 0.73 R C 0.79 S C 0.80 Q C 0.79 R C 0.81 R C 0.70 F C 0.57 V C 0.57 D C 0.65 A C 0.75 D C 0.85 P H 0.91 R H 0.94 Q H 0.95 T H 0.96 V H 0.96 G H 0.96 A H 0.96 L H 0.96 V H 0.96 A H 0.96 I H 0.96 I H 0.95 R H 0.92 E H 0.78 L C 0.53 R C 0.89 P C 0.89 H C 0.83 V E 0.85 V E 0.92 V E 0.92 T E 0.85 Y E 0.54 D C 0.82 P C 0.86 N C 0.90 G C 0.89 G C 0.83 Y C 0.78 G C 0.82 H C 0.81 P C 0.51 D H 0.59 H H 0.91 V H 0.95 H H 0.96 T H 0.96 H H 0.96 T H 0.96 V H 0.96 T H 0.96 T H 0.96 A H 0.96 A H 0.95 V H 0.94 A H 0.90 A H 0.78 A H 0.56 G C 0.66 V C 0.65 G C 0.55 S C 0.55 G C 0.59 T C 0.64 A C 0.62 D C 0.59 H C 0.62 P C 0.71 G C 0.75 D C 0.77 P C 0.74 W C 0.70 T C 0.70 V C 0.61 P C 0.53 K E 0.63 F E 0.78 Y E 0.76 W E 0.77 T E 0.67 V E 0.48 L C 0.60 G C 0.72 L C 0.69 S C 0.52 A H 0.63 L H 0.72 I H 0.69 S H 0.64 G H 0.59 A H 0.63 R H 0.65 A H 0.67 L H 0.64 V H 0.55 P H 0.48 D C 0.54 D C 0.66 L C 0.74 R C 0.78 P C 0.74 E C 0.71 W C 0.65 V C 0.63 L C 0.59 P C 0.51 R C 0.50 A C 0.56 D C 0.67 E C 0.65 I C 0.67 A C 0.74 F C 0.65 G C 0.67 Y C 0.66 S C 0.66 D C 0.69 D C 0.71 G C 0.72 I C 0.67 D C 0.55 A E 0.57 V E 0.79 V E 0.84 E E 0.78 A E 0.48 D C 0.57 E H 0.64 Q H 0.82 A H 0.89 R H 0.93 A H 0.94 A H 0.95 K H 0.96 V H 0.96 A H 0.96 A H 0.96 L H 0.95 A H 0.93 A H 0.87 H H 0.75 A H 0.62 T C 0.48 Q C 0.53 V C 0.49 V C 0.56 V C 0.68 G C 0.78 P C 0.66 T C 0.57 G C 0.42 R E 0.47 A E 0.55 A E 0.59 A E 0.56 L C 0.46 S C 0.65 N C 0.54 N C 0.55 L H 0.43 A C 0.38 L C 0.41 P C 0.41 I C 0.49 L C 0.55 A C 0.53 D C 0.48 E C 0.41 H E 0.38 Y E 0.50 V E 0.55 L E 0.48 A C 0.50 G C 0.65 G C 0.73 S C 0.72 A C 0.69 G C 0.73 A C 0.71 R C 0.72 D C 0.73 E C 0.73 R C 0.70 G C 0.75 W C 0.80 E C 0.53 T C 0.54 D C 0.57 L C 0.53 L E 0.48 A E 0.48 G E 0.54 L E 0.59 G E 0.53 F C 0.49 T C 0.69 A C 0.77 S C 0.82 G C 0.86 T C 0.92 END