PFRMAT SS TARGET T0190 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0190.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0190.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0190.t2k.str.rdb (weight 1.53983) METHOD T0190.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 T0190.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0190 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 T0190.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 36 METHOD METHOD ============================================ METHOD Comments from T0190.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0190 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 T0190.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 36 METHOD METHOD ============================================ METHOD Comments from T0190.t2k.str.rdb METHOD ============================================ METHOD TARGET T0190 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 T0190.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 36 METHOD METHOD ============================================ METHOD Comments from T0190.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0190 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 T0190.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 36 METHOD METHOD ============================================ MODEL 1 A C 0.90 Q C 0.86 Q C 0.86 N C 0.86 I C 0.78 L C 0.52 S E 0.62 V E 0.80 H E 0.86 I E 0.85 L E 0.78 N E 0.62 Q C 0.50 Q C 0.67 T C 0.80 G C 0.86 K C 0.68 P C 0.60 A C 0.74 A C 0.81 D C 0.84 V C 0.64 T E 0.78 V E 0.90 T E 0.92 L E 0.92 E E 0.90 K E 0.87 K E 0.58 A C 0.78 D C 0.91 N C 0.89 G C 0.52 W E 0.72 L E 0.76 Q E 0.80 L E 0.77 N E 0.70 T E 0.65 A E 0.69 K E 0.71 T E 0.64 D C 0.85 K C 0.86 D C 0.91 G C 0.89 R C 0.66 I E 0.54 K C 0.72 A C 0.73 L C 0.71 W C 0.76 P C 0.79 E H 0.50 Q H 0.50 T C 0.50 A C 0.67 T C 0.68 T C 0.60 G E 0.50 D E 0.78 Y E 0.90 R E 0.92 V E 0.92 V E 0.90 F E 0.84 K E 0.60 T C 0.54 G H 0.76 D H 0.87 Y H 0.91 F H 0.92 K H 0.89 K H 0.77 Q C 0.67 N C 0.93 L C 0.91 E C 0.88 S C 0.77 F C 0.65 F C 0.59 P C 0.54 E C 0.50 I E 0.70 P E 0.86 V E 0.90 E E 0.92 F E 0.91 H E 0.88 I E 0.73 N C 0.54 K C 0.83 V C 0.87 N C 0.89 E C 0.77 H E 0.54 Y E 0.82 H E 0.86 V E 0.85 P E 0.81 L E 0.75 L E 0.77 L E 0.59 S C 0.71 Q C 0.74 Y C 0.70 G C 0.64 Y C 0.57 S C 0.53 T C 0.52 Y C 0.56 R C 0.71 G C 0.85 S C 0.91 END