PFRMAT SS TARGET T0419 AUTHOR SAM-T02-server METHOD This file is the result of combining several RDB files, specifically METHOD T0419.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0419.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0419.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 T0419.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0419 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 T0419.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 390 METHOD METHOD ============================================ METHOD Comments from T0419.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0419 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 T0419.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 390 METHOD METHOD ============================================ METHOD Comments from T0419.t2k.str.rdb METHOD ============================================ METHOD TARGET T0419 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 T0419.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 390 METHOD METHOD ============================================ MODEL 1 M C 0.97 F C 0.72 E C 0.59 S C 0.46 A C 0.44 E C 0.58 V C 0.69 G C 0.86 H C 0.83 S C 0.73 I C 0.75 D C 0.93 K H 0.94 D H 0.95 T H 0.96 Y H 0.96 E H 0.94 K H 0.86 A H 0.82 V H 0.74 I H 0.95 E H 0.96 L H 0.97 R H 0.97 E H 0.97 A H 0.97 L H 0.97 L H 0.96 E H 0.96 A H 0.96 Q H 0.96 F H 0.95 E H 0.95 L H 0.95 K H 0.94 Q H 0.88 Q H 0.76 A C 0.56 R C 0.96 F C 0.96 P C 0.77 V E 0.94 I E 0.98 I E 0.98 L E 0.98 I E 0.90 N C 0.55 G C 0.84 I C 0.52 E H 0.60 G H 0.52 A C 0.55 G C 0.71 K H 0.87 G H 0.94 E H 0.97 T H 0.98 V H 0.98 K H 0.97 L H 0.97 L H 0.96 N H 0.95 E H 0.91 W H 0.75 M C 0.52 D C 0.91 P C 0.85 R C 0.83 L C 0.62 I E 0.68 E E 0.85 V E 0.86 Q E 0.77 S E 0.56 F C 0.71 L C 0.88 R C 0.94 P C 0.95 S C 0.93 D H 0.69 E H 0.75 E H 0.85 L H 0.79 E H 0.67 R C 0.59 P C 0.62 P H 0.55 Q H 0.77 W H 0.86 R H 0.88 F H 0.88 W H 0.87 R H 0.74 R H 0.49 L C 0.83 P C 0.92 P C 0.84 K C 0.84 G C 0.79 R E 0.59 T E 0.90 G E 0.94 I E 0.95 F E 0.88 F E 0.54 G C 0.83 N C 0.74 W H 0.51 Y H 0.62 S H 0.74 Q H 0.91 M H 0.94 L H 0.95 Y H 0.95 A H 0.94 R H 0.93 V H 0.88 E H 0.72 G C 0.53 H C 0.66 I C 0.73 K C 0.77 E H 0.80 A H 0.88 K H 0.90 L H 0.94 D H 0.96 Q H 0.96 A H 0.97 I H 0.98 D H 0.97 A H 0.97 A H 0.97 E H 0.97 R H 0.97 F H 0.97 E H 0.97 R H 0.96 M H 0.93 L H 0.89 C H 0.80 D H 0.57 E C 0.74 G C 0.96 A C 0.72 L E 0.78 L E 0.90 F E 0.93 K E 0.91 F E 0.87 W E 0.80 F E 0.74 H E 0.62 L C 0.69 S C 0.88 K H 0.96 K H 0.96 Q H 0.97 L H 0.97 K H 0.97 E H 0.96 R H 0.95 L H 0.95 K H 0.93 A H 0.91 L H 0.85 E H 0.68 K C 0.63 D C 0.93 P C 0.74 Q C 0.67 H C 0.56 S C 0.56 W C 0.46 K C 0.46 L C 0.77 S C 0.91 P H 0.85 L H 0.87 D H 0.91 W H 0.95 K H 0.92 Q H 0.91 S H 0.90 E H 0.89 V H 0.88 Y H 0.90 D H 0.92 R H 0.92 F H 0.95 V H 0.96 H H 0.95 Y H 0.96 G H 0.97 E H 0.97 R H 0.97 V H 0.97 L H 0.96 R H 0.92 R H 0.82 T C 0.49 S C 0.84 R C 0.77 D C 0.78 Y C 0.80 A C 0.88 P C 0.85 W E 0.60 Y E 0.87 V E 0.91 V E 0.84 E E 0.54 G C 0.85 A C 0.94 D C 0.94 E H 0.79 R H 0.88 Y H 0.95 R H 0.95 A H 0.96 L H 0.96 T H 0.97 V H 0.97 G H 0.97 R H 0.97 I H 0.97 L H 0.97 L H 0.97 E H 0.97 G H 0.97 L H 0.97 Q H 0.96 A H 0.93 A H 0.90 L H 0.83 A H 0.66 T C 0.56 K C 0.73 E C 0.74 R C 0.75 A C 0.78 K C 0.77 R C 0.77 Q C 0.78 P C 0.78 H C 0.79 A C 0.79 A C 0.82 P C 0.81 L C 0.83 V C 0.81 S C 0.77 S C 0.78 L C 0.79 D C 0.79 N C 0.76 R C 0.64 G C 0.63 L C 0.57 L C 0.53 D C 0.65 S C 0.75 L C 0.85 D C 0.91 L C 0.70 G C 0.66 Q C 0.64 Y C 0.72 L C 0.79 D C 0.85 K H 0.88 D H 0.94 A H 0.95 Y H 0.96 K H 0.96 E H 0.96 Q H 0.95 L H 0.96 A H 0.96 A H 0.96 E H 0.97 Q H 0.97 A H 0.97 R H 0.97 L H 0.97 A H 0.97 G H 0.97 L H 0.96 I H 0.97 R H 0.96 D H 0.96 K H 0.96 R H 0.94 F H 0.86 R C 0.58 Q C 0.97 H C 0.95 S C 0.64 L E 0.96 V E 0.98 A E 0.98 V E 0.98 F E 0.92 E E 0.71 G C 0.66 N C 0.67 D C 0.61 A C 0.71 A C 0.80 G C 0.90 K C 0.80 G C 0.57 G H 0.67 A H 0.84 I H 0.96 R H 0.96 R H 0.96 V H 0.96 T H 0.95 D H 0.89 A H 0.59 L C 0.68 D C 0.93 P C 0.83 R C 0.80 Q C 0.60 Y E 0.64 H E 0.88 I E 0.93 V E 0.84 P E 0.58 I C 0.75 A C 0.88 A C 0.92 P C 0.96 T C 0.95 E H 0.81 E H 0.83 E H 0.89 R H 0.88 A H 0.82 Q H 0.75 P H 0.70 Y H 0.83 L H 0.92 W H 0.93 R H 0.93 F H 0.91 W H 0.90 R H 0.79 H H 0.62 I C 0.74 P C 0.89 A C 0.86 R C 0.90 R C 0.81 Q E 0.61 F E 0.94 T E 0.96 I E 0.96 F E 0.84 D E 0.49 R C 0.78 S C 0.77 W C 0.58 Y C 0.58 G C 0.62 R C 0.49 V E 0.51 L E 0.59 V E 0.66 E E 0.65 R E 0.53 I E 0.41 E C 0.54 G C 0.68 F C 0.74 C C 0.85 A C 0.96 P H 0.92 A H 0.95 D H 0.96 W H 0.97 L H 0.96 R H 0.94 A H 0.92 Y H 0.92 G H 0.85 E H 0.78 I H 0.81 N H 0.87 D H 0.95 F H 0.96 E H 0.97 E H 0.97 Q H 0.97 L H 0.97 S H 0.96 E H 0.86 Y C 0.62 G C 0.94 I C 0.79 I E 0.77 V E 0.84 V E 0.88 K E 0.87 F E 0.83 W E 0.66 L E 0.62 A E 0.55 I C 0.67 D C 0.92 K H 0.95 Q H 0.96 T H 0.97 Q H 0.97 M H 0.97 E H 0.97 R H 0.96 F H 0.96 K H 0.96 E H 0.94 R H 0.92 E H 0.84 K H 0.63 T C 0.88 P C 0.72 Y C 0.68 K C 0.58 R C 0.69 Y C 0.57 K C 0.54 I C 0.72 T C 0.89 E H 0.86 E H 0.87 D H 0.89 W H 0.95 R H 0.91 N H 0.82 R H 0.81 D H 0.78 K H 0.80 W H 0.88 D H 0.94 Q H 0.96 Y H 0.97 V H 0.97 D H 0.97 A H 0.97 V H 0.98 G H 0.97 D H 0.97 M H 0.96 V H 0.95 D H 0.88 R H 0.68 T C 0.66 S C 0.90 T C 0.92 E C 0.85 I C 0.82 A C 0.88 P C 0.83 W E 0.60 T E 0.89 L E 0.94 V E 0.86 E E 0.60 A C 0.80 N C 0.92 D C 0.85 K H 0.81 R H 0.92 F H 0.96 A H 0.96 R H 0.97 V H 0.97 K H 0.98 V H 0.98 L H 0.98 R H 0.98 T H 0.98 I H 0.97 N H 0.97 D H 0.93 A H 0.89 I H 0.80 E H 0.74 A H 0.69 A H 0.60 Y C 0.55 K C 0.64 K C 0.75 D C 0.86 K C 0.98 END