PFRMAT SS TARGET T0140 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0140.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0140.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0140.t2k.str.rdb (weight 1.53983) METHOD T0140.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 T0140.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0140 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 T0140.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 341 METHOD METHOD ============================================ METHOD Comments from T0140.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0140 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 T0140.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 341 METHOD METHOD ============================================ METHOD Comments from T0140.t2k.str.rdb METHOD ============================================ METHOD TARGET T0140 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 T0140.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 341 METHOD METHOD ============================================ METHOD Comments from T0140.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0140 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 T0140.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 341 METHOD METHOD ============================================ MODEL 1 M C 0.91 R C 0.71 G C 0.66 S C 0.60 H C 0.50 H C 0.49 H C 0.56 H C 0.72 H C 0.83 H C 0.61 G C 0.53 S C 0.44 R E 0.44 L E 0.46 Q C 0.52 S C 0.67 G C 0.62 K C 0.49 M E 0.67 T E 0.75 G E 0.86 I E 0.91 V E 0.92 K E 0.89 W E 0.87 F E 0.79 N E 0.76 A E 0.59 D C 0.46 K C 0.63 G C 0.71 F C 0.56 G E 0.69 F E 0.83 I E 0.81 T E 0.56 P C 0.64 D C 0.74 D C 0.75 G C 0.82 S C 0.61 K E 0.78 D E 0.85 V E 0.87 F E 0.86 V E 0.84 H E 0.76 F E 0.60 S C 0.44 A C 0.60 G C 0.67 S C 0.72 S C 0.49 G H 0.69 A H 0.76 A H 0.75 V H 0.70 R H 0.65 G H 0.54 N C 0.55 P C 0.77 Q C 0.86 Q C 0.87 G C 0.90 D C 0.57 R E 0.83 V E 0.89 E E 0.88 G E 0.87 K E 0.89 I E 0.92 K E 0.87 S E 0.90 I E 0.81 T E 0.64 D C 0.52 F C 0.67 G E 0.55 I E 0.79 F E 0.91 I E 0.90 G E 0.89 L E 0.68 D C 0.68 G C 0.88 G C 0.89 I C 0.61 D E 0.50 G E 0.73 L E 0.86 V E 0.85 H E 0.78 L H 0.39 S H 0.48 D H 0.60 I H 0.51 S C 0.52 W C 0.53 A C 0.53 Q C 0.49 A C 0.56 E C 0.74 A C 0.90 END