PFRMAT SS TARGET T0141 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0141.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0141.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0141.t2k.str.rdb (weight 1.53983) METHOD T0141.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 T0141.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0141 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 T0141.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 58 METHOD METHOD ============================================ METHOD Comments from T0141.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0141 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 T0141.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 58 METHOD METHOD ============================================ METHOD Comments from T0141.t2k.str.rdb METHOD ============================================ METHOD TARGET T0141 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 T0141.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 58 METHOD METHOD ============================================ METHOD Comments from T0141.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0141 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 T0141.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 58 METHOD METHOD ============================================ MODEL 1 M C 0.90 L C 0.73 L C 0.70 D C 0.73 E C 0.73 G C 0.75 W C 0.60 L C 0.48 A C 0.50 E C 0.61 A C 0.59 R C 0.63 R C 0.57 V C 0.73 P C 0.80 S C 0.84 P C 0.79 H C 0.79 Y C 0.70 D C 0.76 C C 0.76 R C 0.83 P C 0.79 D C 0.77 D C 0.76 E C 0.79 N C 0.75 P C 0.73 S C 0.50 L E 0.91 L E 0.93 V E 0.93 V E 0.91 H E 0.77 N C 0.60 I C 0.72 S C 0.82 L C 0.85 P C 0.83 P H 0.56 G H 0.72 E H 0.75 F H 0.75 G H 0.71 G H 0.71 P H 0.76 W H 0.80 I H 0.85 D H 0.86 A H 0.84 L H 0.79 F H 0.62 T C 0.52 G C 0.72 T C 0.77 I C 0.74 D C 0.85 P C 0.76 N C 0.78 A C 0.70 H C 0.73 P C 0.54 Y C 0.48 F H 0.42 A C 0.43 G C 0.52 I C 0.73 A C 0.77 H C 0.81 L C 0.75 R C 0.57 V E 0.70 S E 0.80 A E 0.87 H E 0.90 C E 0.91 L E 0.92 I E 0.90 R E 0.58 R C 0.85 D C 0.93 G C 0.87 E E 0.69 I E 0.91 V E 0.88 Q E 0.90 Y E 0.86 V E 0.73 P C 0.60 F H 0.54 D H 0.57 K H 0.62 R H 0.48 A H 0.41 W H 0.37 H C 0.36 A C 0.52 G C 0.66 V C 0.69 S C 0.66 S C 0.63 Y C 0.64 Q C 0.75 G C 0.81 R C 0.75 E C 0.69 R C 0.67 C C 0.65 N C 0.66 D C 0.69 F C 0.61 S E 0.58 I E 0.73 G E 0.82 I E 0.88 E E 0.88 L E 0.82 E E 0.64 G C 0.69 T C 0.85 D C 0.88 T C 0.85 L C 0.85 A C 0.86 Y C 0.87 T C 0.86 D H 0.94 A H 0.95 Q H 0.96 Y H 0.96 Q H 0.96 Q H 0.95 L H 0.96 A H 0.96 A H 0.96 V H 0.96 T H 0.96 N H 0.96 A H 0.96 L H 0.95 I H 0.93 T H 0.85 R H 0.66 Y C 0.70 P C 0.90 A C 0.88 I C 0.90 A H 0.72 N H 0.74 N H 0.72 M C 0.47 T C 0.53 G C 0.54 H C 0.55 C C 0.56 N C 0.59 I C 0.68 A C 0.84 P C 0.78 E C 0.77 R C 0.68 K C 0.63 T C 0.59 D C 0.78 P C 0.82 G C 0.82 P C 0.82 S C 0.86 F C 0.82 D C 0.80 W H 0.89 A H 0.93 R H 0.94 F H 0.94 R H 0.94 A H 0.89 L H 0.82 V H 0.55 T C 0.78 P C 0.83 S C 0.77 S C 0.72 H C 0.71 K C 0.59 E C 0.61 M C 0.73 T C 0.91 END