PFRMAT SS TARGET T0188 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0188.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0188.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0188.t2k.str.rdb (weight 1.53983) METHOD T0188.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 T0188.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0188 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 T0188.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 38 METHOD METHOD ============================================ METHOD Comments from T0188.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0188 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 T0188.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 38 METHOD METHOD ============================================ METHOD Comments from T0188.t2k.str.rdb METHOD ============================================ METHOD TARGET T0188 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 T0188.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 38 METHOD METHOD ============================================ METHOD Comments from T0188.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0188 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 T0188.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 38 METHOD METHOD ============================================ MODEL 1 M C 0.86 I E 0.65 I E 0.86 A E 0.87 I E 0.85 P E 0.71 V C 0.61 S C 0.80 E C 0.87 N C 0.84 R C 0.82 G C 0.84 K C 0.78 D C 0.80 S C 0.73 P C 0.59 I C 0.52 S C 0.57 E C 0.54 H C 0.54 F C 0.54 G C 0.67 R C 0.69 A C 0.74 P C 0.80 Y E 0.55 F E 0.88 A E 0.92 F E 0.93 V E 0.91 K E 0.90 V E 0.68 K C 0.76 N C 0.90 N C 0.89 A E 0.50 I E 0.85 A E 0.86 D E 0.89 I E 0.84 S E 0.82 V E 0.79 E E 0.69 E E 0.50 N C 0.73 P C 0.76 L C 0.61 A C 0.55 Q C 0.61 D C 0.69 H C 0.78 V C 0.76 H C 0.73 G C 0.57 A C 0.45 V H 0.86 P H 0.92 N H 0.93 F H 0.94 V H 0.94 K H 0.92 E H 0.85 K C 0.61 G C 0.93 A C 0.88 E C 0.57 L E 0.93 V E 0.93 I E 0.93 V E 0.85 R C 0.61 G C 0.78 I C 0.77 G C 0.87 R H 0.61 R H 0.74 A H 0.93 I H 0.95 A H 0.95 A H 0.96 F H 0.95 E H 0.94 A H 0.90 M C 0.64 G C 0.94 V C 0.87 K E 0.64 V E 0.89 I E 0.89 K E 0.86 G C 0.50 A C 0.84 S C 0.90 G C 0.85 T C 0.74 V H 0.90 E H 0.94 E H 0.95 V H 0.95 V H 0.95 N H 0.95 Q H 0.94 Y H 0.92 L H 0.79 S C 0.59 G C 0.81 Q C 0.77 L C 0.64 K C 0.62 D C 0.48 S C 0.57 D C 0.64 Y C 0.73 E C 0.74 V C 0.74 H C 0.77 D C 0.79 H C 0.80 H C 0.81 H C 0.78 H C 0.78 E C 0.76 H C 0.79 H C 0.92 END