PFRMAT SS
TARGET T0419
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0419.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0419.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0419.t04.str2.rdb  (weight 1.54758)
METHOD T0419.t04.alpha.rdb  (weight 0.659012)
METHOD T0419.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0419.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0419.t2k.str2.rdb  (weight 1.54758)
METHOD T0419.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 T0419.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0419
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	    7 (1 EBGHSTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0419.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 39.8416
METHOD
METHOD ============================================
METHOD Comments from T0419.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0419
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	    6 (1 EBGHTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0419.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 39.8416
METHOD
METHOD ============================================
METHOD Comments from T0419.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0419
METHOD Using neural net t04-2621-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 T0419.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 39.8416
METHOD
METHOD ============================================
METHOD Comments from T0419.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0419
METHOD Using neural net t04-2621-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 T0419.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 39.8416
METHOD
METHOD ============================================
METHOD Comments from T0419.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0419
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 T0419.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 390
METHOD
METHOD ============================================
METHOD Comments from T0419.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0419
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 T0419.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 390
METHOD
METHOD ============================================
METHOD Comments from T0419.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0419
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.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 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0419.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 390
METHOD
METHOD ============================================
METHOD Comments from T0419.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0419
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 T0419.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 390
METHOD
METHOD ============================================
MODEL 1
M C 0.69
F C 0.46
E H 0.43
S H 0.41
A C 0.38
E C 0.44
V C 0.60
G C 0.79
H C 0.77
S C 0.72
I C 0.78
D C 0.89
K H 0.93
D H 0.94
T H 0.94
Y H 0.94
E H 0.92
K H 0.83
A H 0.74
V H 0.68
I H 0.93
E H 0.95
L H 0.95
R H 0.96
E H 0.96
A H 0.95
L H 0.95
L H 0.95
E H 0.94
A H 0.94
Q H 0.95
F H 0.94
E H 0.94
L H 0.93
K H 0.91
Q H 0.86
Q H 0.68
A C 0.62
R C 0.91
F C 0.92
P C 0.78
V E 0.90
I E 0.93
I E 0.93
L E 0.93
I E 0.86
N C 0.53
G C 0.77
I C 0.57
E C 0.47
G C 0.55
A C 0.57
G C 0.67
K H 0.78
G H 0.91
E H 0.95
T H 0.96
V H 0.96
K H 0.96
L H 0.95
L H 0.95
N H 0.93
E H 0.88
W H 0.69
M C 0.58
D C 0.86
P C 0.71
R C 0.79
L C 0.67
I E 0.60
E E 0.82
V E 0.86
Q E 0.78
S E 0.66
F C 0.63
L C 0.83
R C 0.89
P C 0.88
S C 0.90
D H 0.66
E H 0.76
E H 0.83
L H 0.79
E H 0.64
R C 0.64
P C 0.72
P H 0.50
Q H 0.69
W H 0.77
R H 0.84
F H 0.87
W H 0.87
R H 0.78
R H 0.56
L C 0.79
P C 0.89
P C 0.84
K C 0.83
G C 0.79
R E 0.51
T E 0.86
G E 0.89
I E 0.90
F E 0.81
F E 0.50
G C 0.77
N C 0.61
W H 0.54
Y H 0.61
S H 0.74
Q H 0.89
M H 0.92
L H 0.93
Y H 0.94
A H 0.92
R H 0.91
V H 0.87
E H 0.66
G C 0.61
H C 0.73
I C 0.72
K C 0.79
E H 0.78
A H 0.86
K H 0.88
L H 0.92
D H 0.95
Q H 0.95
A H 0.96
I H 0.96
D H 0.96
A H 0.95
A H 0.96
E H 0.95
R H 0.95
F H 0.95
E H 0.95
R H 0.95
M H 0.91
L H 0.87
C H 0.79
D H 0.66
E C 0.70
G C 0.92
A C 0.65
L E 0.78
L E 0.87
F E 0.90
K E 0.89
F E 0.87
W E 0.81
F E 0.73
H E 0.61
L C 0.73
S C 0.88
K H 0.90
K H 0.95
Q H 0.95
L H 0.95
K H 0.95
E H 0.95
R H 0.93
L H 0.94
K H 0.92
A H 0.88
L H 0.80
E H 0.67
K C 0.60
D C 0.85
P C 0.66
Q C 0.60
H C 0.47
S C 0.60
W C 0.50
K E 0.55
L C 0.69
S C 0.87
P H 0.84
L H 0.85
D H 0.90
W H 0.94
K H 0.92
Q H 0.90
S H 0.89
E H 0.88
V H 0.85
Y H 0.88
D H 0.90
R H 0.91
F H 0.94
V H 0.95
H H 0.95
Y H 0.95
G H 0.96
E H 0.96
R H 0.96
V H 0.95
L H 0.94
R H 0.90
R H 0.78
T C 0.49
S C 0.79
R C 0.73
D C 0.71
Y C 0.75
A C 0.85
P C 0.79
W E 0.56
Y E 0.82
V E 0.87
V E 0.81
E E 0.57
G C 0.81
A C 0.89
D C 0.88
E H 0.68
R H 0.78
Y H 0.91
R H 0.92
A H 0.93
L H 0.95
T H 0.95
V H 0.95
G H 0.96
R H 0.96
I H 0.96
L H 0.96
L H 0.96
E H 0.96
G H 0.96
L H 0.95
Q H 0.94
A H 0.92
A H 0.88
L H 0.82
A H 0.66
T C 0.56
K C 0.70
E C 0.70
R C 0.69
A C 0.70
K C 0.70
R C 0.72
Q C 0.73
P C 0.74
H C 0.74
A C 0.75
A C 0.78
P C 0.78
L C 0.79
V C 0.78
S C 0.71
S C 0.72
L C 0.72
D C 0.72
N C 0.69
R C 0.59
G C 0.57
L C 0.49
L C 0.50
D C 0.63
S C 0.73
L C 0.81
D C 0.84
L C 0.55
G C 0.55
Q C 0.51
Y C 0.63
L C 0.70
D C 0.82
K H 0.86
D H 0.92
A H 0.94
Y H 0.94
K H 0.95
E H 0.94
Q H 0.94
L H 0.94
A H 0.94
A H 0.94
E H 0.95
Q H 0.95
A H 0.96
R H 0.95
L H 0.96
A H 0.95
G H 0.95
L H 0.95
I H 0.95
R H 0.95
D H 0.95
K H 0.95
R H 0.92
F H 0.84
R C 0.61
Q C 0.94
H C 0.91
S C 0.64
L E 0.91
V E 0.93
A E 0.93
V E 0.92
F E 0.88
E E 0.64
G C 0.67
N C 0.67
D C 0.65
A C 0.73
A C 0.79
G C 0.88
K C 0.72
G C 0.58
G H 0.59
A H 0.81
I H 0.93
R H 0.92
R H 0.93
V H 0.92
T H 0.91
D H 0.83
A H 0.56
L C 0.68
D C 0.86
P C 0.74
R C 0.78
Q C 0.66
Y E 0.63
H E 0.86
I E 0.89
V E 0.82
P E 0.65
I C 0.72
A C 0.87
A C 0.89
P C 0.90
T C 0.91
E H 0.75
E H 0.80
E H 0.85
R H 0.84
A H 0.77
Q H 0.69
P H 0.67
Y H 0.77
L H 0.85
W H 0.85
R H 0.85
F H 0.86
W H 0.86
R H 0.80
H H 0.62
I C 0.70
P C 0.86
A C 0.85
R C 0.85
R C 0.78
Q E 0.66
F E 0.89
T E 0.91
I E 0.89
F E 0.71
D C 0.54
R C 0.71
S C 0.69
W C 0.58
Y C 0.63
G C 0.68
R C 0.53
V E 0.52
L E 0.62
V E 0.63
E E 0.56
R E 0.43
I C 0.49
E C 0.57
G C 0.68
F C 0.69
C C 0.81
A C 0.92
P H 0.91
A H 0.93
D H 0.95
W H 0.95
L H 0.95
R H 0.93
A H 0.92
Y H 0.90
G H 0.84
E H 0.76
I H 0.76
N H 0.80
D H 0.93
F H 0.94
E H 0.96
E H 0.95
Q H 0.95
L H 0.94
S H 0.92
E H 0.83
Y C 0.64
G C 0.90
I C 0.66
I E 0.78
V E 0.84
V E 0.87
K E 0.86
F E 0.83
W E 0.73
L E 0.64
A E 0.46
I C 0.71
D C 0.91
K H 0.90
Q H 0.94
T H 0.94
Q H 0.96
M H 0.95
E H 0.95
R H 0.95
F H 0.95
K H 0.94
E H 0.90
R H 0.86
E H 0.76
K H 0.57
T C 0.80
P C 0.61
Y C 0.55
K H 0.54
R C 0.62
Y C 0.66
K C 0.63
I C 0.79
T C 0.88
E H 0.86
E H 0.86
D H 0.90
W H 0.93
R H 0.90
N H 0.81
R H 0.80
D H 0.79
K H 0.79
W H 0.88
D H 0.94
Q H 0.94
Y H 0.95
V H 0.96
D H 0.95
A H 0.95
V H 0.96
G H 0.96
D H 0.95
M H 0.95
V H 0.93
D H 0.88
R H 0.68
T C 0.59
S C 0.84
T C 0.87
E C 0.76
I C 0.78
A C 0.84
P C 0.77
W E 0.57
T E 0.84
L E 0.88
V E 0.84
E E 0.63
A C 0.77
N C 0.87
D C 0.81
K H 0.77
R H 0.90
F H 0.94
A H 0.95
R H 0.96
V H 0.96
K H 0.96
V H 0.96
L H 0.96
R H 0.96
T H 0.96
I H 0.96
N H 0.95
D H 0.93
A H 0.90
I H 0.85
E H 0.81
A H 0.74
A H 0.61
Y C 0.55
K C 0.65
K C 0.74
D C 0.78
K C 0.90
END