PFRMAT SS TARGET T0481 AUTHOR SAM-T02-server METHOD This file is the result of combining several RDB files, specifically METHOD T0481.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0481.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0481.t2k.str.rdb (weight 1.53983) 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 T0481.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0481 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 T0481.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 141 METHOD METHOD ============================================ METHOD Comments from T0481.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0481 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 T0481.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 141 METHOD METHOD ============================================ METHOD Comments from T0481.t2k.str.rdb METHOD ============================================ METHOD TARGET T0481 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 T0481.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 141 METHOD METHOD ============================================ MODEL 1 M C 0.96 C C 0.83 Q C 0.54 S H 0.87 N H 0.90 Q H 0.92 I H 0.92 V H 0.95 S H 0.94 H H 0.93 F H 0.93 L H 0.94 S H 0.92 H H 0.93 R H 0.94 N H 0.96 V H 0.96 T H 0.97 N H 0.98 E H 0.97 L H 0.97 A H 0.96 E H 0.87 K H 0.64 I C 0.85 S C 0.93 K H 0.72 D H 0.75 H H 0.82 Y H 0.51 S C 0.67 Y C 0.69 K C 0.80 P C 0.85 A C 0.87 E C 0.86 T C 0.89 S C 0.86 M C 0.82 S C 0.85 A H 0.94 E H 0.96 E H 0.97 L H 0.97 V H 0.97 K H 0.97 H H 0.97 I H 0.97 L H 0.96 T H 0.96 S H 0.96 F H 0.97 H H 0.97 L H 0.97 F H 0.97 A H 0.97 N H 0.95 V H 0.92 I H 0.85 K H 0.66 E C 0.61 G C 0.85 N C 0.81 A C 0.74 S C 0.76 P C 0.73 F C 0.74 Q C 0.72 N C 0.76 K C 0.84 Q C 0.87 E C 0.86 E C 0.86 T C 0.87 E H 0.94 T H 0.96 D H 0.97 L H 0.97 N H 0.97 V H 0.96 L H 0.94 A H 0.95 K H 0.94 T H 0.93 Y H 0.93 T H 0.95 E H 0.96 K H 0.97 T H 0.97 V H 0.97 A H 0.97 I H 0.96 L H 0.94 E H 0.80 Q H 0.54 L C 0.82 T C 0.92 E H 0.77 E H 0.77 Q H 0.82 L H 0.73 D H 0.60 R H 0.57 E H 0.41 I C 0.43 D C 0.49 L C 0.71 T C 0.78 S C 0.83 A C 0.83 F C 0.82 G C 0.81 R C 0.79 K C 0.74 V C 0.76 T C 0.79 G H 0.96 R H 0.97 A H 0.97 L H 0.98 L H 0.97 Q H 0.97 L H 0.96 A H 0.96 M H 0.95 E H 0.94 H H 0.91 E H 0.91 I H 0.92 H H 0.89 H H 0.87 K H 0.90 G H 0.92 N H 0.97 L H 0.98 F H 0.98 V H 0.98 Y H 0.98 V H 0.97 R H 0.97 E H 0.91 M H 0.52 G C 0.97 H C 0.96 T C 0.88 E C 0.92 L C 0.88 P C 0.59 F E 0.53 Y C 0.49 Q C 0.63 Q C 0.79 R C 0.91 M C 0.98 END