PFRMAT SS TARGET T0132 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0132.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0132.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0132.t2k.str.rdb (weight 1.53983) METHOD T0132.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 T0132.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0132 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 T0132.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 89 METHOD METHOD ============================================ METHOD Comments from T0132.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0132 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 T0132.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 89 METHOD METHOD ============================================ METHOD Comments from T0132.t2k.str.rdb METHOD ============================================ METHOD TARGET T0132 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 T0132.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 89 METHOD METHOD ============================================ METHOD Comments from T0132.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0132 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 T0132.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 89 METHOD METHOD ============================================ MODEL 1 M C 0.90 S C 0.77 A C 0.71 N C 0.71 F C 0.75 T C 0.79 D C 0.77 K C 0.75 N C 0.59 G C 0.52 R C 0.50 Q C 0.67 S C 0.74 K C 0.81 G C 0.78 V E 0.65 L E 0.87 L E 0.89 L E 0.91 R E 0.89 T E 0.85 L E 0.80 A E 0.66 M C 0.61 P C 0.65 S C 0.59 D C 0.55 T C 0.68 N C 0.79 A C 0.70 N C 0.73 G C 0.67 D C 0.38 I H 0.42 F H 0.54 G H 0.73 G H 0.83 W H 0.95 I H 0.95 M H 0.95 S H 0.95 Q H 0.94 M H 0.95 D H 0.95 M H 0.96 G H 0.96 G H 0.96 A H 0.96 I H 0.96 L H 0.96 A H 0.96 K H 0.95 E H 0.90 I H 0.79 A C 0.56 H C 0.85 G C 0.88 R C 0.72 V E 0.66 V E 0.86 T E 0.91 V E 0.88 A E 0.85 V E 0.71 E C 0.48 S E 0.45 M E 0.78 N E 0.81 F E 0.80 I E 0.72 K E 0.56 P E 0.56 I E 0.59 S C 0.60 V C 0.79 G C 0.90 D C 0.70 V E 0.81 V E 0.92 C E 0.93 C E 0.92 Y E 0.90 G E 0.90 Q E 0.91 C E 0.91 L E 0.86 K E 0.84 V E 0.55 G C 0.69 R C 0.68 S E 0.56 S E 0.82 I E 0.91 K E 0.93 I E 0.92 K E 0.93 V E 0.93 E E 0.93 V E 0.91 W E 0.88 V E 0.75 K E 0.47 K C 0.57 V C 0.56 A C 0.63 S C 0.71 E C 0.79 P C 0.79 I C 0.76 G C 0.75 E C 0.53 R E 0.56 Y E 0.70 C E 0.78 V E 0.79 T E 0.82 D E 0.88 A E 0.90 V E 0.92 F E 0.93 T E 0.92 F E 0.92 V E 0.90 A E 0.84 V E 0.77 D C 0.77 N C 0.86 N C 0.93 G C 0.92 R C 0.81 S E 0.59 R C 0.60 T C 0.66 I C 0.77 P C 0.81 R C 0.83 E C 0.82 N C 0.74 N C 0.78 Q C 0.82 E C 0.88 L C 0.89 E H 0.90 K H 0.92 A H 0.94 L H 0.94 A H 0.93 L H 0.92 I H 0.87 S H 0.81 E H 0.66 Q C 0.54 P C 0.67 L C 0.90 END