PFRMAT SS TARGET T0151 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0151.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0151.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0151.t2k.str.rdb (weight 1.53983) METHOD T0151.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 T0151.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0151 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 T0151.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 147 METHOD METHOD ============================================ METHOD Comments from T0151.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0151 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 T0151.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 147 METHOD METHOD ============================================ METHOD Comments from T0151.t2k.str.rdb METHOD ============================================ METHOD TARGET T0151 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 T0151.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 147 METHOD METHOD ============================================ METHOD Comments from T0151.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0151 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 T0151.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 147 METHOD METHOD ============================================ MODEL 1 M C 0.81 A C 0.73 G C 0.70 D C 0.69 T C 0.64 T E 0.72 I E 0.91 T E 0.92 I E 0.92 V E 0.81 G E 0.70 N E 0.58 L C 0.54 T C 0.68 A C 0.78 D C 0.86 P C 0.66 E C 0.51 L E 0.57 R E 0.67 F E 0.76 T C 0.70 P C 0.84 S C 0.93 G C 0.93 A C 0.73 A E 0.77 V E 0.89 A E 0.92 N E 0.92 F E 0.92 T E 0.92 V E 0.90 A E 0.80 S E 0.66 T C 0.56 P C 0.65 R C 0.60 I C 0.56 Y C 0.58 D C 0.70 R C 0.79 Q C 0.85 T C 0.85 G C 0.79 E C 0.51 W E 0.51 K E 0.46 D C 0.45 G C 0.58 E C 0.59 A C 0.49 L E 0.60 F E 0.76 L E 0.82 R E 0.84 C E 0.85 N E 0.86 I E 0.73 W C 0.51 R C 0.57 E H 0.60 A H 0.86 A H 0.92 E H 0.94 N H 0.93 V H 0.93 A H 0.93 E H 0.90 S H 0.82 L H 0.62 T C 0.58 R C 0.79 G C 0.91 A C 0.84 R E 0.64 V E 0.87 I E 0.91 V E 0.91 S E 0.83 G E 0.83 R E 0.86 L E 0.85 K E 0.82 Q E 0.81 R E 0.62 S E 0.70 F E 0.74 E E 0.77 T C 0.59 R C 0.81 E C 0.91 G C 0.88 E C 0.53 K E 0.87 R E 0.85 T E 0.87 V E 0.86 I E 0.89 E E 0.92 V E 0.92 E E 0.91 V E 0.87 D E 0.74 E E 0.73 I E 0.68 G E 0.67 P E 0.54 S C 0.49 L C 0.58 R C 0.62 Y C 0.61 A C 0.64 T C 0.65 A C 0.64 K C 0.67 V C 0.69 N C 0.71 K C 0.71 A C 0.69 S C 0.71 R C 0.69 S C 0.70 G C 0.70 G C 0.70 F C 0.68 G C 0.71 S C 0.72 G C 0.71 S C 0.72 R C 0.71 P C 0.71 A C 0.72 P C 0.70 A C 0.68 Q C 0.69 T C 0.70 S C 0.67 S C 0.66 A C 0.67 S C 0.69 G C 0.71 D C 0.73 D C 0.75 P C 0.74 W C 0.73 G C 0.70 S C 0.72 A C 0.73 P C 0.77 A C 0.76 S C 0.79 G C 0.80 S C 0.74 F C 0.72 G C 0.73 G C 0.71 G C 0.72 D C 0.68 D C 0.74 E C 0.78 P C 0.83 P C 0.85 F C 0.91 END