PFRMAT SS TARGET T0181 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0181.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0181.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0181.t2k.str.rdb (weight 1.53983) METHOD T0181.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 T0181.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0181 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 T0181.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 2 METHOD METHOD ============================================ METHOD Comments from T0181.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0181 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 T0181.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 2 METHOD METHOD ============================================ METHOD Comments from T0181.t2k.str.rdb METHOD ============================================ METHOD TARGET T0181 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 T0181.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 2 METHOD METHOD ============================================ METHOD Comments from T0181.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0181 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 T0181.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 2 METHOD METHOD ============================================ MODEL 1 M C 0.90 S C 0.78 T C 0.68 V C 0.56 T E 0.54 K E 0.71 Y E 0.76 F E 0.77 Y E 0.71 K C 0.52 G C 0.73 E C 0.80 N C 0.81 T C 0.61 D E 0.62 L E 0.89 I E 0.91 V E 0.91 F E 0.87 A E 0.66 A C 0.68 S C 0.85 E C 0.73 E H 0.51 L H 0.62 V H 0.74 D H 0.77 E H 0.76 Y H 0.69 L H 0.52 K C 0.58 N C 0.84 P C 0.76 S C 0.73 I C 0.64 G C 0.64 K C 0.50 L H 0.71 S H 0.77 E H 0.71 V H 0.66 V H 0.50 E H 0.41 L E 0.45 F E 0.65 E E 0.73 V E 0.76 F E 0.75 T E 0.54 P C 0.68 Q C 0.81 D C 0.86 G C 0.86 R C 0.81 G C 0.82 A C 0.77 E C 0.65 G C 0.59 E C 0.46 L H 0.35 G H 0.37 A H 0.45 A H 0.49 S H 0.48 K H 0.83 A H 0.84 Q H 0.86 V H 0.84 E H 0.81 N H 0.74 E H 0.66 F C 0.50 G C 0.74 K C 0.71 G C 0.64 K C 0.52 K H 0.45 I H 0.82 E H 0.90 E H 0.91 V H 0.93 I H 0.94 D H 0.94 L H 0.94 I H 0.94 L H 0.91 R H 0.78 N C 0.61 G C 0.90 K C 0.87 P C 0.80 N C 0.82 S C 0.76 T C 0.68 T C 0.57 S C 0.53 S C 0.49 L C 0.42 K C 0.45 T C 0.54 K C 0.71 G C 0.80 G C 0.80 N C 0.73 A C 0.65 G C 0.66 T C 0.56 K C 0.50 A C 0.54 Y C 0.72 N C 0.92 END