PFRMAT SS
TARGET YGR204W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR204W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR204W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR204W.t2k.str2.rdb  (weight 1.54758)
METHOD YGR204W.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 YGR204W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR204W
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 YGR204W.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 311
METHOD
METHOD ============================================
METHOD Comments from YGR204W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR204W
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 YGR204W.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 311
METHOD
METHOD ============================================
METHOD Comments from YGR204W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR204W
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 YGR204W.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 311
METHOD
METHOD ============================================
METHOD Comments from YGR204W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR204W
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 YGR204W.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 311
METHOD
METHOD ============================================
MODEL 1
M C 0.80
A C 0.59
G C 0.48
Q E 0.58
V E 0.64
L E 0.51
D C 0.75
G C 0.61
K H 0.88
A H 0.93
C H 0.95
A H 0.96
Q H 0.95
Q H 0.95
F H 0.96
R H 0.96
S H 0.95
N H 0.95
I H 0.95
A H 0.96
N H 0.96
E H 0.96
I H 0.96
K H 0.96
S H 0.95
I H 0.95
Q H 0.93
G H 0.90
H H 0.73
V C 0.75
P C 0.82
G C 0.86
F C 0.82
A C 0.87
P C 0.80
N C 0.58
L E 0.85
A E 0.92
I E 0.93
I E 0.91
Q E 0.83
V E 0.52
G C 0.84
N C 0.91
R C 0.88
P H 0.54
D H 0.63
S H 0.73
A H 0.80
T H 0.81
Y H 0.82
V H 0.87
R H 0.88
M H 0.88
K H 0.92
R H 0.94
K H 0.95
A H 0.95
A H 0.94
E H 0.91
E H 0.80
A C 0.53
G C 0.91
I C 0.71
V E 0.71
A E 0.85
N E 0.87
F E 0.86
I E 0.75
H E 0.73
L C 0.64
D C 0.84
E C 0.76
S C 0.83
A C 0.79
T C 0.86
E H 0.93
F H 0.95
E H 0.96
V H 0.96
L H 0.96
R H 0.96
Y H 0.96
V H 0.95
D H 0.95
Q H 0.90
L H 0.82
N H 0.60
E C 0.62
D C 0.86
P C 0.82
H C 0.89
T C 0.83
H C 0.80
G E 0.79
I E 0.92
I E 0.92
V E 0.91
Q E 0.73
L C 0.63
P C 0.70
L C 0.78
P C 0.75
A C 0.66
H C 0.67
L C 0.75
D C 0.77
E H 0.84
D H 0.88
R H 0.90
I H 0.91
T H 0.88
S H 0.82
R H 0.70
V C 0.52
L C 0.81
A H 0.50
E H 0.49
K C 0.54
D C 0.67
V C 0.70
D C 0.80
G C 0.79
F C 0.70
G C 0.71
P H 0.57
T H 0.68
N H 0.71
I H 0.82
G H 0.81
E H 0.82
L H 0.83
N H 0.74
K C 0.56
K C 0.83
N C 0.81
G C 0.76
H C 0.79
P C 0.80
F C 0.75
F C 0.69
L C 0.75
P C 0.77
C C 0.76
T C 0.85
P H 0.90
K H 0.94
G H 0.95
I H 0.96
I H 0.96
E H 0.96
L H 0.96
L H 0.96
H H 0.94
K H 0.88
A C 0.54
N C 0.93
V C 0.90
T C 0.81
I C 0.69
E C 0.73
G C 0.77
S C 0.63
R E 0.72
S E 0.90
V E 0.93
V E 0.92
I E 0.81
G C 0.55
R C 0.82
S C 0.75
D C 0.61
I C 0.62
V C 0.71
G C 0.76
S H 0.54
P H 0.90
V H 0.95
A H 0.95
E H 0.95
L H 0.95
L H 0.93
K H 0.84
S H 0.68
L C 0.70
N C 0.93
S C 0.81
T E 0.73
V E 0.89
T E 0.90
I E 0.89
T E 0.79
H E 0.49
S C 0.72
K C 0.78
T C 0.80
R C 0.83
D C 0.83
I H 0.81
A H 0.90
S H 0.91
Y H 0.89
L H 0.77
H H 0.61
D C 0.62
A C 0.80
D C 0.87
I E 0.87
V E 0.93
V E 0.93
V E 0.89
A E 0.62
I C 0.77
G C 0.85
Q C 0.83
P C 0.64
E C 0.65
F C 0.55
V C 0.60
K C 0.73
G H 0.75
E H 0.73
W H 0.70
F C 0.54
K C 0.61
P C 0.52
R C 0.58
D C 0.57
G C 0.59
T C 0.51
S C 0.48
S C 0.54
D C 0.68
K C 0.88
K C 0.87
T E 0.61
V E 0.90
V E 0.92
I E 0.91
D E 0.82
V E 0.52
G C 0.56
T C 0.58
N C 0.65
Y C 0.52
V C 0.63
A C 0.72
D C 0.80
P C 0.72
S C 0.68
K C 0.71
K C 0.77
S C 0.84
G C 0.84
F C 0.52
K E 0.71
C E 0.77
V E 0.65
G E 0.59
D E 0.49
V C 0.61
E C 0.76
F H 0.79
N H 0.83
E H 0.87
A H 0.88
I H 0.89
K H 0.85
Y H 0.79
V H 0.62
H H 0.54
L H 0.47
I E 0.37
T C 0.57
P C 0.76
V C 0.84
P C 0.84
G C 0.88
G C 0.80
V C 0.72
G C 0.52
P H 0.88
M H 0.94
T H 0.96
V H 0.96
A H 0.96
M H 0.96
L H 0.96
M H 0.96
Q H 0.96
N H 0.96
T H 0.96
L H 0.96
I H 0.96
A H 0.96
A H 0.96
K H 0.95
R H 0.94
Q H 0.91
M H 0.88
E H 0.81
E H 0.69
S C 0.59
S C 0.84
K C 0.88
P C 0.76
L C 0.65
Q C 0.49
I E 0.53
P C 0.55
P C 0.66
L C 0.79
P C 0.70
L C 0.63
K C 0.66
L C 0.72
L C 0.75
T C 0.79
P C 0.76
V C 0.79
P C 0.68
S C 0.59
D H 0.90
I H 0.93
D H 0.94
I H 0.93
S H 0.88
R H 0.78
A H 0.62
Q C 0.69
Q C 0.82
P C 0.78
K C 0.73
L C 0.67
I H 0.91
N H 0.94
Q H 0.95
L H 0.95
A H 0.95
Q H 0.93
E H 0.88
L C 0.53
G C 0.93
I C 0.93
Y C 0.92
S H 0.77
H H 0.81
E H 0.81
L H 0.54
E H 0.40
L H 0.37
Y C 0.50
G C 0.63
H C 0.52
Y E 0.48
K E 0.67
A E 0.74
K E 0.79
I E 0.69
S C 0.57
P H 0.71
K H 0.81
V H 0.83
I H 0.81
E H 0.70
R H 0.72
L H 0.61
Q C 0.52
T C 0.78
R C 0.88
Q C 0.86
N C 0.91
G C 0.88
K E 0.60
Y E 0.92
I E 0.93
L E 0.93
V E 0.91
S E 0.85
G E 0.72
I C 0.52
T C 0.78
P C 0.81
T C 0.85
P C 0.81
L C 0.76
G C 0.73
E C 0.74
G C 0.76
K C 0.71
S C 0.60
T H 0.50
T H 0.67
T H 0.91
M H 0.94
G H 0.94
L H 0.95
V H 0.95
Q H 0.95
A H 0.95
L H 0.95
T H 0.91
A H 0.80
H H 0.63
L C 0.70
G C 0.92
K C 0.87
P C 0.68
A E 0.69
I E 0.83
A E 0.87
N E 0.87
V E 0.79
R E 0.68
Q C 0.56
P C 0.65
S C 0.71
L C 0.74
G C 0.79
P C 0.69
T C 0.58
L C 0.55
G C 0.69
V C 0.68
K C 0.70
G C 0.72
G C 0.73
A C 0.69
A C 0.75
G C 0.77
G C 0.69
G C 0.67
Y E 0.51
S E 0.65
Q E 0.75
V E 0.72
I C 0.49
P C 0.74
M H 0.84
D H 0.86
E H 0.85
F H 0.72
N H 0.58
L H 0.57
H H 0.59
L H 0.55
T C 0.59
G C 0.70
D C 0.56
I H 0.74
H H 0.82
A H 0.90
I H 0.92
G H 0.91
A H 0.92
A H 0.93
N H 0.94
N H 0.95
L H 0.96
L H 0.96
A H 0.96
A H 0.95
A H 0.95
I H 0.95
D H 0.93
T H 0.90
R H 0.87
M H 0.85
F H 0.79
H H 0.73
E H 0.67
T H 0.51
T C 0.57
Q H 0.52
K H 0.55
N H 0.55
D H 0.91
A H 0.91
T H 0.92
F H 0.91
Y H 0.88
N H 0.76
R H 0.67
L C 0.49
V C 0.75
P C 0.67
R C 0.50
K C 0.53
N C 0.72
G C 0.75
K C 0.67
R C 0.63
K C 0.65
F C 0.70
T C 0.80
P H 0.57
S H 0.61
M H 0.59
Q H 0.56
R H 0.49
R H 0.57
L H 0.64
N H 0.51
R C 0.62
L C 0.74
G C 0.69
I C 0.61
Q C 0.73
K C 0.71
T C 0.72
N C 0.83
P C 0.82
D C 0.84
D C 0.84
L C 0.84
T C 0.87
P H 0.73
E H 0.75
E H 0.80
I H 0.80
N H 0.73
K H 0.51
F C 0.69
A C 0.71
R C 0.59
L C 0.67
N C 0.73
I C 0.73
D C 0.82
P C 0.65
D C 0.63
T C 0.43
I E 0.70
T E 0.77
I E 0.78
K E 0.65
R E 0.63
V E 0.49
V C 0.47
D C 0.58
I H 0.47
N H 0.49
D H 0.69
R H 0.90
M H 0.89
L H 0.88
R H 0.84
Q H 0.70
I H 0.67
T H 0.54
I H 0.42
G C 0.54
Q C 0.71
A C 0.79
P C 0.71
T C 0.74
E C 0.75
K C 0.86
N C 0.85
H C 0.65
T E 0.61
R C 0.60
V C 0.70
T C 0.82
G C 0.73
F C 0.48
D E 0.59
I E 0.51
T H 0.39
V H 0.72
A H 0.83
S H 0.85
E H 0.93
L H 0.95
M H 0.95
A H 0.96
I H 0.96
L H 0.95
A H 0.93
L H 0.86
S H 0.69
K C 0.62
D C 0.82
L H 0.92
R H 0.95
D H 0.93
M H 0.95
K H 0.94
E H 0.90
R H 0.78
I H 0.69
G C 0.58
R C 0.66
V E 0.58
V E 0.79
V E 0.86
A E 0.84
A E 0.78
D C 0.63
V C 0.86
N C 0.93
R C 0.94
S C 0.77
P E 0.77
V E 0.79
T E 0.65
V H 0.66
E H 0.65
D H 0.64
V H 0.54
G C 0.54
C H 0.66
T H 0.86
G H 0.91
A H 0.94
L H 0.95
T H 0.95
A H 0.95
L H 0.93
L H 0.93
R H 0.92
D H 0.84
A H 0.71
I C 0.54
K C 0.73
P C 0.66
N C 0.66
L C 0.43
M E 0.44
Q E 0.48
T C 0.45
L C 0.61
E C 0.79
G C 0.85
T C 0.84
P C 0.65
V E 0.65
L E 0.78
V E 0.69
H C 0.46
A C 0.76
G C 0.79
P C 0.64
F C 0.53
A C 0.48
N C 0.50
I C 0.51
S C 0.57
I C 0.67
G C 0.74
A C 0.63
S C 0.57
S H 0.65
V H 0.81
I H 0.91
A H 0.93
D H 0.94
R H 0.95
V H 0.95
A H 0.94
L H 0.91
K H 0.87
L H 0.74
V C 0.49
G C 0.85
T C 0.85
E C 0.78
P C 0.65
E C 0.55
A C 0.50
K H 0.47
T C 0.47
E C 0.54
A C 0.80
G C 0.87
Y E 0.78
V E 0.90
V E 0.88
T E 0.76
E C 0.54
A C 0.74
G C 0.71
F C 0.68
D C 0.66
F C 0.63
T C 0.60
M C 0.51
G C 0.54
G H 0.51
E H 0.48
R H 0.53
F H 0.55
F H 0.53
N H 0.48
I H 0.76
K H 0.82
C H 0.80
R H 0.76
S H 0.71
S C 0.57
G C 0.90
L C 0.88
T C 0.84
P C 0.81
N C 0.85
A E 0.59
V E 0.76
V E 0.87
L E 0.72
V E 0.45
A H 0.68
T H 0.76
V H 0.85
R H 0.90
A H 0.91
L H 0.87
K H 0.77
S H 0.58
H C 0.74
G C 0.85
G C 0.84
A C 0.78
P C 0.72
D C 0.59
V C 0.52
K C 0.87
P C 0.88
G C 0.92
Q C 0.84
P C 0.74
L C 0.73
P C 0.71
S H 0.60
A H 0.63
Y H 0.52
T C 0.63
E C 0.53
E C 0.53
N C 0.55
I H 0.94
E H 0.96
F H 0.96
V H 0.96
E H 0.95
K H 0.73
G C 0.57
A H 0.52
A H 0.73
N H 0.74
M H 0.90
C H 0.95
K H 0.95
Q H 0.95
I H 0.95
A H 0.95
N H 0.94
I H 0.92
K H 0.91
Q H 0.83
F C 0.59
G C 0.93
V C 0.92
P C 0.81
V E 0.77
V E 0.91
V E 0.92
A E 0.91
I E 0.88
N E 0.63
K C 0.72
F C 0.79
E C 0.81
T C 0.87
D C 0.84
T C 0.82
E H 0.94
G H 0.95
E H 0.96
I H 0.96
A H 0.96
A H 0.96
I H 0.96
R H 0.96
K H 0.96
A H 0.96
A H 0.96
L H 0.94
E H 0.89
A C 0.65
G C 0.94
A C 0.87
F C 0.56
E E 0.65
A E 0.80
V E 0.83
T E 0.77
S E 0.55
N H 0.51
H H 0.65
W H 0.71
A H 0.72
E C 0.53
G C 0.76
G C 0.68
K H 0.51
G H 0.60
A H 0.93
I H 0.96
D H 0.96
L H 0.96
A H 0.96
K H 0.96
A H 0.96
V H 0.96
I H 0.95
E H 0.94
A H 0.90
S H 0.78
N C 0.52
Q C 0.79
P C 0.79
V C 0.77
D C 0.75
F C 0.65
H C 0.60
F C 0.54
L C 0.60
Y C 0.74
D C 0.80
V C 0.79
N C 0.86
S C 0.88
S C 0.81
V H 0.88
E H 0.94
D H 0.95
K H 0.96
L H 0.96
T H 0.96
T H 0.96
I H 0.96
V H 0.96
Q H 0.95
K H 0.92
M H 0.83
Y H 0.52
G C 0.79
G C 0.85
A C 0.84
A C 0.82
I C 0.68
D C 0.57
I C 0.75
L C 0.90
P H 0.89
E H 0.93
A H 0.95
Q H 0.96
R H 0.95
K H 0.95
I H 0.96
D H 0.96
M H 0.96
Y H 0.96
K H 0.95
E H 0.92
Q H 0.61
G C 0.83
F C 0.84
G C 0.77
N C 0.75
L C 0.80
P C 0.64
I E 0.52
C E 0.58
I E 0.64
A E 0.57
K C 0.44
T C 0.59
Q C 0.65
Y C 0.69
S C 0.73
L C 0.67
S C 0.70
H C 0.80
D C 0.80
A H 0.64
T H 0.66
L H 0.79
K H 0.51
G C 0.84
V C 0.87
P C 0.85
T C 0.80
G C 0.78
F E 0.50
T E 0.77
F E 0.74
P E 0.61
I E 0.52
R E 0.55
D E 0.67
V E 0.73
R E 0.79
L E 0.67
S C 0.45
N C 0.67
G C 0.84
A C 0.75
G C 0.63
Y E 0.80
L E 0.76
Y E 0.63
A E 0.50
L C 0.41
A C 0.44
A C 0.44
E H 0.45
I C 0.43
Q C 0.51
T C 0.57
I C 0.79
P C 0.86
G C 0.86
L C 0.87
A C 0.85
T C 0.81
Y C 0.83
A C 0.73
G C 0.58
Y C 0.43
M C 0.48
A C 0.54
V C 0.53
E C 0.54
V E 0.58
D C 0.85
D C 0.87
D C 0.92
G C 0.88
E C 0.64
I E 0.73
D E 0.59
G E 0.56
L C 0.56
F C 0.89
END