PFRMAT SS
TARGET T0409
AUTHOR 4008-1775-0004 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0409.t06.str2.rdb  (weight 1.54425)
METHOD T0409.t06.str4.rdb  (weight 0.924988)
METHOD T0409.t06.pb.rdb  (weight 0.789901)
METHOD T0409.t06.bys.rdb  (weight 0.748322)
METHOD T0409.t06.alpha.rdb  (weight 0.678173)
METHOD T0409.t04.str2.rdb  (weight 1.54425)
METHOD T0409.t04.str4.rdb  (weight 0.924988)
METHOD T0409.t04.pb.rdb  (weight 0.789901)
METHOD T0409.t04.bys.rdb  (weight 0.748322)
METHOD T0409.t04.alpha.rdb  (weight 0.678173)
METHOD T0409.t2k.str2.rdb  (weight 1.54425)
METHOD T0409.t2k.str4.rdb  (weight 0.924988)
METHOD T0409.t2k.pb.rdb  (weight 0.789901)
METHOD T0409.t2k.bys.rdb  (weight 0.748322)
METHOD T0409.t2k.alpha.rdb  (weight 0.678173)
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 T0409.t06.str2.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   13 (1 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t06-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 26.3911
METHOD
METHOD ============================================
METHOD Comments from T0409.t06.str4.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   21 (1 str4 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t06-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 26.3911
METHOD
METHOD ============================================
METHOD Comments from T0409.t06.pb.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   16 (1 pb )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t06-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 26.3911
METHOD
METHOD ============================================
METHOD Comments from T0409.t06.bys.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   11 (1 Bystroff )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t06-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 26.3911
METHOD
METHOD ============================================
METHOD Comments from T0409.t06.alpha.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   11 (1 ABCDEFGHIST )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t06-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 26.3911
METHOD
METHOD ============================================
METHOD Comments from T0409.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   13 (1 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 24.6872
METHOD
METHOD ============================================
METHOD Comments from T0409.t04.str4.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   21 (1 str4 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 24.6872
METHOD
METHOD ============================================
METHOD Comments from T0409.t04.pb.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   16 (1 pb )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 24.6872
METHOD
METHOD ============================================
METHOD Comments from T0409.t04.bys.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   11 (1 Bystroff )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 24.6872
METHOD
METHOD ============================================
METHOD Comments from T0409.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   11 (1 ABCDEFGHIST )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 24.6872
METHOD
METHOD ============================================
METHOD Comments from T0409.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   13 (1 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t2k-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 33.5932
METHOD
METHOD ============================================
METHOD Comments from T0409.t2k.str4.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   21 (1 str4 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t2k-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 33.5932
METHOD
METHOD ============================================
METHOD Comments from T0409.t2k.pb.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   16 (1 pb )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t2k-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 33.5932
METHOD
METHOD ============================================
METHOD Comments from T0409.t2k.bys.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   11 (1 Bystroff )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t2k-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 33.5932
METHOD
METHOD ============================================
METHOD Comments from T0409.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0409
METHOD Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   11 (1 ABCDEFGHIST )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0409.t2k-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 33.5932
METHOD
METHOD ============================================
MODEL 1
Y C 0.66
R C 0.78
G C 0.77
P H 0.48
E H 0.57
A H 0.56
F H 0.50
L C 0.40
K C 0.57
L C 0.70
P C 0.65
K C 0.51
D C 0.50
L H 0.65
K H 0.69
D H 0.73
R H 0.87
E H 0.89
A H 0.92
L H 0.92
Q H 0.92
D H 0.92
I H 0.91
M H 0.89
Q H 0.83
D H 0.54
I C 0.66
G C 0.69
N C 0.70
S C 0.63
D C 0.59
D C 0.62
I C 0.59
L C 0.53
A E 0.46
A E 0.69
V E 0.78
V E 0.74
L E 0.70
S E 0.67
A E 0.49
T C 0.69
P C 0.63
G C 0.73
A E 0.53
V E 0.72
E E 0.79
A E 0.80
F E 0.78
R E 0.67
K C 0.55
N C 0.78
G C 0.82
E C 0.58
T E 0.70
I E 0.78
R E 0.80
I E 0.74
T C 0.51
G C 0.59
D C 0.59
G C 0.53
L H 0.57
K H 0.77
A H 0.83
A H 0.84
H H 0.84
R H 0.82
F H 0.68
L C 0.47
S C 0.61
N C 0.65
D C 0.71
P C 0.53
K C 0.58
I C 0.67
G C 0.65
E C 0.57
K C 0.56
R C 0.48
I E 0.52
R C 0.67
P C 0.67
G C 0.79
A C 0.54
L E 0.75
I E 0.80
R E 0.81
V E 0.80
K E 0.76
K E 0.67
T C 0.55
E C 0.58
K C 0.72
G C 0.74
S C 0.51
W E 0.68
Q E 0.75
I E 0.76
V E 0.73
Q E 0.66
L C 0.59
P C 0.75
END