PFRMAT SS
TARGET T0529
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0529.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0529.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0529.t04.str2.rdb  (weight 1.54758)
METHOD T0529.t04.alpha.rdb  (weight 0.659012)
METHOD T0529.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0529.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0529.t2k.str2.rdb  (weight 1.54758)
METHOD T0529.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 T0529.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0529
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 T0529.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 4.63776
METHOD
METHOD ============================================
METHOD Comments from T0529.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0529
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 T0529.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 4.63776
METHOD
METHOD ============================================
METHOD Comments from T0529.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0529
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 T0529.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 4.63776
METHOD
METHOD ============================================
METHOD Comments from T0529.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0529
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 T0529.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 4.63776
METHOD
METHOD ============================================
METHOD Comments from T0529.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0529
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 T0529.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 49
METHOD
METHOD ============================================
METHOD Comments from T0529.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0529
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 T0529.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 49
METHOD
METHOD ============================================
METHOD Comments from T0529.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0529
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 T0529.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 49
METHOD
METHOD ============================================
METHOD Comments from T0529.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0529
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 T0529.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 49
METHOD
METHOD ============================================
MODEL 1
M C 0.82
S C 0.76
A C 0.77
S C 0.75
K C 0.68
E C 0.62
I C 0.69
K C 0.71
S C 0.59
F H 0.42
L H 0.53
W H 0.67
T H 0.81
Q H 0.85
S H 0.85
L H 0.85
R H 0.84
R H 0.79
E H 0.62
L C 0.49
S C 0.60
G C 0.62
Y C 0.58
C C 0.62
S C 0.59
N C 0.48
I H 0.53
K H 0.72
L H 0.85
Q H 0.89
V H 0.92
V H 0.95
K H 0.95
D H 0.95
A H 0.95
Q H 0.95
A H 0.95
L H 0.93
L H 0.86
H H 0.59
G C 0.48
L C 0.70
D C 0.79
F H 0.77
S H 0.81
E H 0.84
V H 0.86
S H 0.89
N H 0.91
V H 0.94
Q H 0.95
R H 0.95
L H 0.94
M H 0.91
R H 0.86
K H 0.80
E H 0.62
R C 0.54
R C 0.71
D C 0.80
D H 0.59
N H 0.72
D H 0.77
L H 0.91
K H 0.92
R H 0.90
L H 0.91
R H 0.91
D H 0.89
L H 0.87
N H 0.82
Q H 0.83
A H 0.81
V H 0.76
N H 0.67
N H 0.63
L H 0.59
V H 0.42
E E 0.50
L E 0.45
K E 0.37
S C 0.36
T C 0.42
Q C 0.44
Q C 0.49
K C 0.65
S C 0.50
I E 0.81
L E 0.85
R E 0.81
V E 0.51
G C 0.70
T C 0.78
L C 0.84
T C 0.88
S H 0.86
D H 0.89
D H 0.92
L H 0.95
L H 0.95
I H 0.94
L H 0.92
A H 0.88
A H 0.78
D H 0.72
L H 0.92
E H 0.93
K H 0.92
L H 0.93
K H 0.93
S H 0.91
K H 0.85
V H 0.74
I H 0.51
R C 0.56
T C 0.69
E C 0.74
R C 0.83
P C 0.83
L C 0.87
S C 0.87
A C 0.81
G C 0.73
V E 0.44
Y E 0.53
M C 0.49
G C 0.65
N C 0.72
L C 0.73
S C 0.71
S H 0.84
Q H 0.87
Q H 0.91
L H 0.94
D H 0.93
Q H 0.94
R H 0.95
R H 0.96
A H 0.96
L H 0.96
L H 0.96
N H 0.94
M H 0.91
I H 0.70
G C 0.67
M C 0.77
S C 0.74
G C 0.78
G C 0.76
N C 0.76
Q C 0.78
G C 0.77
A C 0.77
R C 0.72
A C 0.74
G C 0.81
R C 0.80
D C 0.85
G C 0.71
V E 0.77
V E 0.87
R E 0.89
V E 0.84
W E 0.73
D E 0.59
V C 0.61
K C 0.80
N C 0.83
A H 0.63
E H 0.73
L H 0.79
L H 0.65
N H 0.55
N C 0.50
Q C 0.48
F C 0.56
G C 0.58
T C 0.51
M H 0.50
P H 0.75
S H 0.85
L H 0.86
T H 0.87
L H 0.88
A H 0.89
C H 0.86
L H 0.79
T H 0.70
K H 0.61
Q C 0.56
G C 0.81
Q C 0.73
V C 0.58
D C 0.53
L H 0.65
N H 0.66
D H 0.73
A H 0.92
V H 0.95
Q H 0.94
A H 0.94
L H 0.93
T H 0.88
D H 0.74
L H 0.54
G C 0.60
L C 0.53
I E 0.41
Y E 0.57
T E 0.64
A E 0.50
K C 0.65
Y C 0.81
P C 0.88
N C 0.88
T H 0.58
S H 0.61
D H 0.74
L H 0.92
D H 0.92
R H 0.90
L H 0.89
T H 0.85
Q H 0.70
S H 0.54
H C 0.73
P C 0.64
I C 0.47
L H 0.44
N C 0.43
M E 0.43
I E 0.48
D C 0.61
T H 0.44
K C 0.46
K H 0.51
S C 0.50
S C 0.50
L C 0.54
N C 0.62
I C 0.66
S C 0.70
G C 0.70
Y C 0.64
N C 0.54
F C 0.49
S C 0.51
L H 0.72
G H 0.80
A H 0.84
A H 0.81
V H 0.81
K H 0.77
A H 0.59
G C 0.61
A C 0.56
C C 0.38
M E 0.43
L C 0.39
D C 0.61
G C 0.77
G C 0.76
N C 0.68
M C 0.57
L C 0.49
E C 0.46
T E 0.54
I E 0.66
K E 0.71
V E 0.58
S C 0.81
P C 0.71
Q C 0.72
T C 0.71
M H 0.88
D H 0.95
G H 0.95
I H 0.96
L H 0.95
K H 0.95
S H 0.93
I H 0.90
L H 0.84
K H 0.78
V H 0.65
K H 0.63
K H 0.59
A H 0.49
L C 0.61
G C 0.82
M C 0.64
F E 0.58
I E 0.61
S C 0.63
D C 0.76
T C 0.87
P C 0.85
G C 0.87
E C 0.82
R C 0.76
N C 0.77
P H 0.72
Y H 0.84
E H 0.86
N H 0.87
I H 0.86
L H 0.83
Y H 0.80
K H 0.78
I H 0.72
C H 0.58
L C 0.42
S C 0.70
G C 0.80
D C 0.78
G C 0.77
W C 0.72
P C 0.65
Y C 0.47
I C 0.48
A C 0.55
S C 0.61
R C 0.58
T C 0.58
S C 0.47
I C 0.39
T C 0.53
G C 0.58
R C 0.52
A C 0.48
W C 0.53
E C 0.53
N C 0.54
T E 0.50
V E 0.62
V E 0.62
D C 0.50
L C 0.66
E C 0.82
S C 0.84
D C 0.85
G C 0.80
K C 0.82
P C 0.81
Q C 0.85
K C 0.83
A C 0.83
D C 0.81
S C 0.78
N C 0.76
N C 0.81
S C 0.85
S C 0.85
K C 0.80
S C 0.74
L C 0.75
Q C 0.72
S C 0.63
A C 0.68
G C 0.72
F C 0.71
T C 0.66
A C 0.71
G C 0.79
L C 0.87
T C 0.88
Y H 0.92
S H 0.94
Q H 0.96
L H 0.96
M H 0.96
T H 0.96
L H 0.96
K H 0.96
D H 0.96
A H 0.95
M H 0.91
L H 0.80
Q H 0.51
L C 0.75
D C 0.89
P C 0.85
N C 0.90
A C 0.84
K C 0.72
T E 0.70
W E 0.84
M E 0.85
D E 0.75
I E 0.51
E C 0.61
G C 0.74
R C 0.86
P C 0.86
E C 0.90
D C 0.87
P C 0.67
V E 0.51
E E 0.72
I E 0.82
A E 0.86
L E 0.85
Y E 0.79
Q E 0.69
P C 0.67
S C 0.84
S C 0.88
G C 0.89
C C 0.72
Y E 0.80
I E 0.88
H E 0.88
F E 0.83
F E 0.72
R C 0.49
E C 0.73
P C 0.71
T C 0.72
D C 0.70
L H 0.70
K H 0.72
Q H 0.68
F H 0.53
K C 0.46
Q C 0.67
D C 0.72
A C 0.70
K C 0.54
Y C 0.50
S C 0.50
H C 0.52
G C 0.47
I E 0.34
D E 0.37
V H 0.51
T H 0.54
D H 0.49
L H 0.68
F H 0.63
A H 0.54
T C 0.48
Q C 0.66
P C 0.49
G H 0.57
L H 0.82
T H 0.89
S H 0.86
A H 0.87
V H 0.86
I H 0.87
D H 0.79
A H 0.56
L C 0.78
P C 0.88
R C 0.85
N C 0.85
M E 0.57
V E 0.89
I E 0.92
T E 0.88
C E 0.71
Q C 0.73
G C 0.85
S C 0.68
D H 0.61
D H 0.80
I H 0.94
R H 0.95
K H 0.95
L H 0.94
L H 0.93
E H 0.91
S H 0.78
Q C 0.52
G C 0.85
R C 0.79
K C 0.62
D C 0.55
I C 0.48
K E 0.61
L E 0.86
I E 0.85
D E 0.82
I E 0.73
A E 0.63
L C 0.67
S C 0.88
K H 0.68
T H 0.85
D H 0.88
S H 0.91
R H 0.89
K H 0.87
Y H 0.86
E H 0.89
N H 0.91
A H 0.93
V H 0.94
W H 0.94
D H 0.93
Q H 0.87
Y H 0.74
K H 0.71
D H 0.77
L H 0.81
C H 0.76
H H 0.64
M C 0.51
H C 0.75
T C 0.87
G C 0.69
V E 0.71
V E 0.84
V E 0.73
E E 0.58
K E 0.59
K E 0.56
K C 0.51
R C 0.77
G C 0.90
G C 0.89
K C 0.84
E C 0.85
E C 0.87
I C 0.77
T C 0.82
P C 0.55
H H 0.47
C H 0.53
A H 0.51
L H 0.68
M H 0.66
D H 0.70
C H 0.76
I H 0.81
M H 0.79
F H 0.81
D H 0.79
A H 0.74
A H 0.68
V H 0.55
S C 0.58
G C 0.82
G C 0.84
L C 0.78
N C 0.86
T C 0.82
S C 0.79
V C 0.81
L C 0.66
R C 0.52
A C 0.51
V C 0.62
L C 0.79
P C 0.78
R C 0.49
D H 0.49
M E 0.40
V E 0.66
F E 0.68
R E 0.49
T C 0.77
S C 0.86
T C 0.86
P C 0.81
R E 0.52
V E 0.75
V E 0.57
L C 0.89
END