PFRMAT SS TARGET T0194 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0194.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0194.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0194.t2k.str.rdb (weight 1.53983) METHOD T0194.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 T0194.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0194 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 T0194.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 43 METHOD METHOD ============================================ METHOD Comments from T0194.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0194 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 T0194.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 43 METHOD METHOD ============================================ METHOD Comments from T0194.t2k.str.rdb METHOD ============================================ METHOD TARGET T0194 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 T0194.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 43 METHOD METHOD ============================================ METHOD Comments from T0194.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0194 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 T0194.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 43 METHOD METHOD ============================================ MODEL 1 M C 0.59 A H 0.51 N H 0.55 A H 0.54 P H 0.58 K C 0.54 G C 0.82 V C 0.83 K C 0.81 F C 0.82 S C 0.78 T C 0.75 S C 0.81 Q C 0.86 T C 0.86 T C 0.88 E H 0.86 E H 0.93 I H 0.95 V H 0.96 R H 0.96 A H 0.96 K H 0.95 V H 0.95 S H 0.95 E H 0.93 L H 0.90 V H 0.82 E H 0.52 Q C 0.77 Y C 0.88 D C 0.87 L E 0.83 I E 0.93 I E 0.93 G E 0.93 I E 0.91 P E 0.81 I E 0.51 D C 0.68 K C 0.60 E C 0.62 I C 0.54 S C 0.48 A H 0.69 S H 0.86 Y H 0.93 A H 0.94 N H 0.94 W H 0.96 K H 0.95 L H 0.94 V H 0.93 E H 0.91 K H 0.84 D H 0.69 Y C 0.55 A C 0.80 S C 0.84 K C 0.67 F E 0.79 H E 0.91 V E 0.90 L E 0.82 D E 0.50 A C 0.70 R C 0.61 A H 0.56 V H 0.63 E H 0.64 M H 0.77 I H 0.85 I H 0.92 D H 0.94 W H 0.95 L H 0.96 I H 0.96 N H 0.96 D H 0.96 I H 0.96 K H 0.96 G H 0.96 W H 0.95 L H 0.94 N H 0.88 T C 0.63 N C 0.92 P C 0.87 Y C 0.85 S C 0.87 R H 0.90 E H 0.94 G H 0.95 L H 0.96 D H 0.96 R H 0.96 F H 0.95 V H 0.95 E H 0.95 Q H 0.91 Y H 0.87 R H 0.77 K H 0.54 K C 0.72 T C 0.73 A C 0.49 A E 0.88 V E 0.92 L E 0.92 F E 0.89 V E 0.72 T C 0.58 D C 0.68 T H 0.54 K H 0.72 P H 0.73 L H 0.71 V H 0.59 A C 0.51 G C 0.74 G C 0.73 R C 0.63 L C 0.58 S C 0.56 N H 0.66 L H 0.82 K H 0.87 S H 0.83 F H 0.85 I H 0.89 I H 0.88 K H 0.84 S H 0.80 L C 0.47 K C 0.62 F C 0.56 H H 0.39 L H 0.46 L H 0.45 I H 0.45 S H 0.42 F E 0.38 L E 0.46 G C 0.84 E C 0.84 N C 0.91 G C 0.87 K C 0.60 L E 0.79 Q E 0.67 F E 0.53 F H 0.42 D H 0.45 K H 0.55 A H 0.46 R H 0.50 S C 0.55 A H 0.72 H H 0.91 D H 0.93 A H 0.95 H H 0.96 K H 0.96 L H 0.96 A H 0.96 V H 0.96 K H 0.96 F H 0.95 L H 0.95 K H 0.94 K H 0.88 Q H 0.79 L H 0.65 L H 0.54 K C 0.53 H C 0.66 S C 0.74 A C 0.76 K C 0.82 L C 0.73 K C 0.51 R E 0.60 G E 0.79 A E 0.89 F E 0.91 L E 0.91 T E 0.89 T E 0.78 V C 0.53 F C 0.78 D C 0.83 E C 0.49 Q H 0.77 T H 0.82 N H 0.89 T H 0.93 N H 0.93 L H 0.94 V H 0.95 Q H 0.95 E H 0.95 F H 0.94 D H 0.91 K H 0.80 L H 0.60 L C 0.61 D C 0.76 H C 0.75 S C 0.68 I C 0.56 N E 0.47 I E 0.57 E E 0.65 Q E 0.71 S E 0.68 L E 0.59 L C 0.52 S C 0.64 P C 0.47 V E 0.56 I E 0.61 C E 0.71 T E 0.66 H E 0.61 T C 0.44 G C 0.81 L C 0.87 N C 0.90 S C 0.50 Y E 0.84 V E 0.92 I E 0.92 V E 0.91 L E 0.86 Q E 0.73 G C 0.66 E C 0.92 END