PFRMAT SS
TARGET YGR217W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR217W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR217W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR217W.t2k.str2.rdb  (weight 1.54758)
METHOD YGR217W.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 YGR217W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR217W
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 YGR217W.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 178
METHOD
METHOD ============================================
METHOD Comments from YGR217W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR217W
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 YGR217W.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 178
METHOD
METHOD ============================================
METHOD Comments from YGR217W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR217W
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 YGR217W.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 178
METHOD
METHOD ============================================
METHOD Comments from YGR217W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR217W
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 YGR217W.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 178
METHOD
METHOD ============================================
MODEL 1
M C 0.85
Q C 0.74
G C 0.77
R C 0.77
K C 0.72
R C 0.66
T C 0.65
L C 0.64
T C 0.70
E C 0.75
P C 0.80
F C 0.78
E C 0.85
P C 0.82
N C 0.83
T C 0.79
N C 0.83
P C 0.80
F C 0.82
G C 0.78
D C 0.72
N C 0.60
A C 0.40
A E 0.43
V E 0.51
M E 0.49
T E 0.54
E E 0.50
N C 0.45
V C 0.61
E C 0.74
D C 0.82
N C 0.83
S C 0.76
E C 0.72
T C 0.74
D C 0.73
G C 0.75
N C 0.71
R C 0.60
L C 0.58
E C 0.64
S C 0.72
K C 0.80
P C 0.81
Q C 0.73
A C 0.69
L C 0.75
V C 0.82
P C 0.82
P C 0.79
A C 0.71
L C 0.73
N C 0.75
I C 0.79
V C 0.82
P C 0.75
P C 0.75
E C 0.73
S C 0.78
S C 0.74
I C 0.71
H C 0.70
S C 0.68
T C 0.68
E C 0.69
E C 0.72
K C 0.72
K C 0.75
G C 0.79
D C 0.67
E C 0.55
Y C 0.65
N C 0.76
G C 0.82
N C 0.84
D C 0.82
K C 0.80
D C 0.79
S C 0.75
S C 0.70
L C 0.66
I C 0.74
S C 0.75
N C 0.79
I C 0.76
F C 0.70
R C 0.60
T C 0.67
R C 0.66
V C 0.73
G C 0.79
R C 0.83
S C 0.81
S C 0.80
H C 0.82
E C 0.78
N C 0.75
L C 0.77
S C 0.82
R C 0.77
P C 0.51
K H 0.45
L H 0.42
S C 0.44
L C 0.56
K C 0.68
T C 0.68
A C 0.64
S C 0.83
F C 0.68
G C 0.67
A H 0.57
A H 0.61
E H 0.56
S C 0.48
S C 0.56
R C 0.66
R C 0.66
N C 0.74
V C 0.76
S C 0.84
P C 0.80
S C 0.82
T C 0.79
K C 0.67
S C 0.65
A C 0.68
K C 0.75
S C 0.83
S C 0.72
S C 0.75
Q C 0.74
Y C 0.79
I C 0.65
D C 0.58
L C 0.53
N C 0.53
D H 0.52
E H 0.50
R H 0.47
L C 0.43
R C 0.47
R C 0.48
R C 0.52
S C 0.61
F C 0.69
S C 0.75
S C 0.80
Y C 0.81
S C 0.83
R C 0.79
S C 0.77
S C 0.75
S C 0.76
R C 0.75
R C 0.77
V C 0.76
S C 0.78
N C 0.79
S C 0.81
P C 0.77
S C 0.76
S C 0.72
T C 0.72
D C 0.73
R C 0.75
P C 0.74
P C 0.65
R C 0.60
S C 0.61
A C 0.66
K C 0.67
V C 0.67
L C 0.66
S C 0.65
L H 0.63
I H 0.73
A H 0.71
A H 0.64
D C 0.54
D C 0.71
M C 0.66
D C 0.60
D C 0.49
F H 0.65
E H 0.66
D H 0.62
L H 0.60
Q H 0.54
K C 0.50
G C 0.67
F C 0.65
K C 0.65
S C 0.64
A C 0.66
I C 0.67
D C 0.75
E C 0.75
E C 0.79
G C 0.79
L C 0.73
T C 0.63
W C 0.61
L C 0.69
P C 0.54
Q C 0.53
L C 0.46
K C 0.48
S C 0.53
E C 0.53
K C 0.56
S C 0.64
R C 0.68
P C 0.68
V C 0.58
S C 0.56
D C 0.56
V C 0.66
G C 0.72
E C 0.69
D C 0.67
R C 0.59
G C 0.56
E C 0.48
G C 0.48
E C 0.50
Q C 0.51
E C 0.55
S C 0.59
I C 0.57
P C 0.54
D C 0.47
V H 0.51
H H 0.47
T C 0.48
P C 0.56
N C 0.68
V C 0.68
G C 0.67
A C 0.64
S C 0.67
A C 0.69
T C 0.74
P C 0.63
G C 0.61
S C 0.60
I C 0.59
H C 0.68
L C 0.73
T C 0.80
P C 0.80
E C 0.83
P C 0.80
A C 0.80
Q C 0.75
N C 0.72
G C 0.56
S C 0.56
V C 0.53
S C 0.66
E C 0.67
G C 0.68
L C 0.75
E C 0.73
G C 0.63
S C 0.59
I C 0.65
N C 0.76
N C 0.80
S C 0.82
R C 0.82
K C 0.60
K C 0.58
P C 0.59
S C 0.70
P C 0.75
K C 0.75
F C 0.73
F H 0.47
H C 0.50
H C 0.57
L C 0.75
S C 0.83
P C 0.54
Q C 0.46
K H 0.43
E C 0.53
D C 0.70
K C 0.75
D C 0.77
Q C 0.61
T E 0.59
E E 0.73
V E 0.70
I E 0.48
E C 0.61
Y C 0.54
A H 0.49
E H 0.52
D H 0.51
I H 0.49
L H 0.45
D H 0.43
F H 0.41
E C 0.45
T C 0.49
L C 0.49
Q C 0.51
R H 0.50
K C 0.50
L C 0.59
E C 0.70
S C 0.76
R C 0.78
P C 0.78
F C 0.77
V C 0.77
L C 0.80
Y C 0.78
G C 0.72
H C 0.60
S E 0.49
L E 0.65
G E 0.74
V E 0.66
F C 0.55
S C 0.84
P C 0.86
T C 0.87
N C 0.81
P H 0.78
L H 0.86
R H 0.92
I H 0.95
K H 0.94
I H 0.95
A H 0.95
R H 0.94
F H 0.91
L H 0.85
L H 0.69
H C 0.68
R C 0.51
R H 0.78
Y H 0.89
S H 0.88
L H 0.95
L H 0.96
Y H 0.96
N H 0.96
T H 0.96
L H 0.96
L H 0.96
T H 0.96
F H 0.95
Y H 0.95
A H 0.95
I H 0.94
L H 0.92
L H 0.89
A H 0.80
I H 0.59
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T C 0.79
Y C 0.81
N C 0.87
P C 0.83
H C 0.82
N C 0.81
V C 0.78
V C 0.71
F C 0.67
L C 0.74
Y C 0.82
R C 0.72
F C 0.69
S C 0.56
N H 0.48
W H 0.59
T H 0.69
D H 0.78
Y H 0.85
F H 0.89
I H 0.91
F H 0.92
I H 0.94
L H 0.93
S H 0.94
A H 0.95
C H 0.94
F H 0.94
T H 0.94
G H 0.95
N H 0.96
D H 0.96
I H 0.96
A H 0.96
K H 0.96
I H 0.95
I H 0.95
A H 0.92
F H 0.82
G H 0.70
F H 0.69
W H 0.58
D C 0.44
D C 0.53
S H 0.75
E H 0.82
M H 0.80
F H 0.78
K H 0.70
A H 0.52
Y C 0.73
G C 0.71
R C 0.64
E H 0.50
Y H 0.53
K H 0.49
S H 0.45
I H 0.51
L H 0.43
Q C 0.50
R C 0.65
S C 0.78
G C 0.84
I C 0.55
M C 0.39
K H 0.47
L H 0.44
Y E 0.43
I E 0.57
Y E 0.60
L E 0.52
R E 0.46
E H 0.37
K C 0.61
Y C 0.82
G C 0.83
R C 0.70
K C 0.56
L C 0.46
I E 0.47
D C 0.59
F C 0.55
I C 0.55
I C 0.69
P C 0.66
F C 0.53
R E 0.47
I E 0.47
I C 0.52
S C 0.77
P C 0.80
G C 0.85
E C 0.84
E C 0.87
T C 0.84
K C 0.72
Y C 0.64
Q C 0.51
R E 0.43
S E 0.44
S E 0.51
L E 0.56
S E 0.52
T C 0.50
S C 0.67
L C 0.67
T C 0.71
K C 0.73
P C 0.63
Y C 0.58
G C 0.68
A H 0.47
K H 0.62
E H 0.66
N H 0.58
Q H 0.54
R C 0.50
P C 0.56
F C 0.70
G C 0.75
T C 0.77
P C 0.73
R C 0.59
A C 0.49
F C 0.39
A C 0.44
R C 0.58
S C 0.74
S C 0.65
W C 0.64
N C 0.51
R H 0.68
I H 0.76
D H 0.79
L H 0.86
V H 0.90
S H 0.91
S H 0.93
V H 0.93
S H 0.94
F H 0.93
W H 0.93
L H 0.92
G H 0.90
M H 0.83
F H 0.72
L H 0.71
S H 0.60
I H 0.54
K C 0.49
S C 0.62
Y C 0.67
D C 0.75
T C 0.78
K C 0.74
T C 0.58
G C 0.52
I E 0.38
R H 0.44
I H 0.54
F H 0.56
K H 0.56
P H 0.64
L H 0.68
A H 0.70
I H 0.72
L H 0.72
R H 0.71
I H 0.74
L H 0.74
R H 0.68
L H 0.64
V H 0.48
N C 0.48
V C 0.60
D C 0.76
T C 0.72
G C 0.71
M H 0.90
P H 0.95
S H 0.96
I H 0.96
L H 0.96
R H 0.96
G H 0.96
L H 0.95
K H 0.95
Y H 0.91
G H 0.84
I H 0.80
P H 0.80
Q H 0.83
L H 0.92
V H 0.94
N H 0.95
V H 0.96
S H 0.96
S H 0.96
M H 0.96
L H 0.96
V H 0.96
Y H 0.96
F H 0.96
W H 0.96
I H 0.96
F H 0.96
F H 0.96
G H 0.96
I H 0.95
L H 0.95
G H 0.94
V H 0.95
Q H 0.94
I H 0.91
F H 0.86
Q H 0.81
G H 0.71
S H 0.73
F H 0.66
R H 0.52
R H 0.45
Q C 0.40
C E 0.39
V E 0.46
W E 0.44
F C 0.63
N C 0.78
P C 0.81
E C 0.80
D C 0.81
P C 0.75
T C 0.72
D C 0.66
T C 0.63
Y C 0.58
Q C 0.56
Y C 0.58
D C 0.56
M C 0.51
Q C 0.51
F C 0.58
C C 0.67
G C 0.73
G C 0.71
Y C 0.59
L C 0.53
D C 0.61
P C 0.68
V C 0.70
T C 0.73
K C 0.72
R C 0.68
K C 0.71
Q C 0.66
N C 0.54
Y C 0.54
I C 0.65
Y C 0.70
E C 0.75
D C 0.78
G C 0.81
S C 0.80
E C 0.75
G C 0.77
S C 0.70
V C 0.75
S C 0.87
K C 0.86
G C 0.85
F C 0.60
L E 0.62
C E 0.52
P C 0.61
Q C 0.67
Y C 0.66
S C 0.66
K C 0.51
C C 0.45
V C 0.50
S C 0.55
N C 0.66
A C 0.68
N C 0.78
P C 0.81
Y C 0.81
N C 0.80
G C 0.81
R C 0.58
I C 0.54
S C 0.59
F H 0.52
D H 0.63
N H 0.78
I H 0.88
V H 0.93
N H 0.95
S H 0.95
M H 0.96
E H 0.96
L H 0.95
V H 0.95
F H 0.95
V H 0.93
I H 0.90
M H 0.84
S H 0.73
A H 0.79
N H 0.82
T H 0.85
F H 0.95
T H 0.96
D H 0.96
L H 0.96
M H 0.96
Y H 0.95
Y H 0.93
T H 0.88
M H 0.66
D C 0.61
S C 0.72
D C 0.81
E C 0.79
M C 0.56
A H 0.61
A H 0.77
C H 0.91
L H 0.94
F H 0.95
F H 0.95
I H 0.96
V H 0.96
C H 0.96
I H 0.95
F H 0.95
V H 0.95
L H 0.95
T H 0.95
I H 0.95
W H 0.96
L H 0.96
L H 0.96
N H 0.96
L H 0.96
L H 0.96
I H 0.95
A H 0.95
V H 0.95
L H 0.93
V H 0.89
S H 0.83
S H 0.82
F H 0.90
E H 0.91
I H 0.92
A H 0.92
N H 0.91
E H 0.90
E H 0.91
Y H 0.91
K H 0.88
K H 0.87
K H 0.87
K H 0.84
F H 0.87
I H 0.87
Y H 0.88
G H 0.89
S H 0.89
R H 0.90
K H 0.91
T H 0.90
G H 0.90
Y H 0.90
V H 0.92
A H 0.92
R H 0.90
I H 0.87
V H 0.80
T H 0.64
G C 0.58
Y C 0.66
W C 0.56
K C 0.41
Y H 0.42
F H 0.42
K H 0.41
L H 0.46
K H 0.47
A C 0.44
N C 0.47
Q H 0.49
T H 0.52
K C 0.48
F C 0.57
P C 0.58
N C 0.50
W C 0.41
S E 0.34
Q E 0.47
K E 0.55
G E 0.65
L E 0.69
A E 0.67
I E 0.51
Y C 0.62
S C 0.50
H H 0.69
V H 0.87
E H 0.93
F H 0.95
I H 0.96
F H 0.96
V H 0.96
I H 0.96
L H 0.96
I H 0.96
I H 0.96
C H 0.95
D H 0.95
I H 0.94
G H 0.94
M H 0.93
R H 0.90
A H 0.87
S H 0.81
V H 0.73
K H 0.51
V C 0.71
S C 0.84
T C 0.82
S C 0.75
A H 0.68
N H 0.70
C H 0.83
N H 0.86
N H 0.86
I H 0.87
L H 0.85
L H 0.81
K H 0.76
T H 0.67
D H 0.64
R H 0.67
G H 0.69
I H 0.76
S H 0.83
I H 0.85
V H 0.88
L H 0.90
F H 0.92
I H 0.92
E H 0.92
S H 0.94
L H 0.95
A H 0.95
R H 0.95
L H 0.95
V H 0.94
L H 0.92
Y H 0.88
L H 0.73
P H 0.51
N C 0.77
M H 0.75
W H 0.86
K H 0.86
F H 0.82
L H 0.71
T H 0.63
K C 0.46
P C 0.60
S C 0.72
Y C 0.68
V C 0.49
Y C 0.55
D C 0.55
F E 0.62
I E 0.73
I E 0.73
S E 0.68
I E 0.49
I H 0.47
T H 0.43
L H 0.56
V H 0.56
I H 0.60
S H 0.60
C H 0.54
L H 0.59
A H 0.53
V H 0.49
E C 0.47
G C 0.71
V C 0.78
L C 0.83
G C 0.74
H C 0.69
M C 0.54
Y H 0.43
A H 0.55
W H 0.88
L H 0.91
S H 0.93
I H 0.94
F H 0.94
H H 0.95
I H 0.95
S H 0.95
R H 0.95
F H 0.95
Y H 0.95
R H 0.95
V H 0.94
I H 0.92
I H 0.82
S H 0.73
F H 0.83
N H 0.91
L H 0.92
T H 0.95
K H 0.96
K H 0.96
L H 0.96
W H 0.96
K H 0.96
Q H 0.95
I H 0.93
L H 0.90
S H 0.83
N H 0.81
G H 0.92
V H 0.94
M H 0.95
I H 0.96
W H 0.96
N H 0.96
L H 0.96
S H 0.96
S H 0.96
F H 0.96
Y H 0.96
F H 0.96
F H 0.96
F H 0.96
T H 0.96
F H 0.96
L H 0.96
V H 0.96
A H 0.96
I H 0.95
I H 0.94
M H 0.93
A H 0.91
V H 0.88
Y H 0.80
F H 0.58
E C 0.71
G C 0.74
V C 0.70
I C 0.69
P C 0.80
P C 0.76
E C 0.76
E C 0.77
M C 0.84
A C 0.81
D C 0.80
Q C 0.76
P C 0.65
F C 0.62
G C 0.70
M C 0.51
Y H 0.50
S H 0.56
L H 0.87
P H 0.94
N H 0.94
S H 0.95
F H 0.95
L H 0.96
S H 0.96
L H 0.96
F H 0.95
I H 0.94
I H 0.89
G H 0.72
S C 0.51
T C 0.78
E C 0.58
N C 0.60
W H 0.78
T H 0.88
D H 0.92
I H 0.92
L H 0.93
Y H 0.94
A H 0.95
L H 0.94
Q H 0.94
K H 0.90
H H 0.81
S C 0.50
P C 0.84
N C 0.84
I C 0.74
S C 0.71
S H 0.56
T H 0.73
F H 0.90
F H 0.94
C H 0.96
S H 0.96
V H 0.96
F H 0.96
F H 0.96
I H 0.96
I H 0.96
W H 0.96
F H 0.96
L H 0.95
L H 0.95
S H 0.94
N H 0.94
S H 0.95
V H 0.96
I H 0.96
L H 0.96
N H 0.95
I H 0.95
F H 0.96
I H 0.96
A H 0.95
L H 0.95
I H 0.92
S H 0.84
E H 0.71
S H 0.49
M C 0.52
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G C 0.65
V C 0.67
N C 0.72
N C 0.74
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R C 0.73
M C 0.68
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Q C 0.65
D C 0.65
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E C 0.62
P C 0.72
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P C 0.67
I C 0.63
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N C 0.73
N C 0.75
D C 0.69
D C 0.66
S C 0.59
A H 0.57
N H 0.52
D H 0.54
L H 0.54
I C 0.52
D C 0.69
R C 0.90
END