PFRMAT SS
TARGET YGR009C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR009C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR009C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR009C.t2k.str2.rdb  (weight 1.54758)
METHOD YGR009C.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 YGR009C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR009C
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 YGR009C.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 40
METHOD
METHOD ============================================
METHOD Comments from YGR009C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR009C
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 YGR009C.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 40
METHOD
METHOD ============================================
METHOD Comments from YGR009C.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR009C
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 YGR009C.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 40
METHOD
METHOD ============================================
METHOD Comments from YGR009C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR009C
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 YGR009C.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 40
METHOD
METHOD ============================================
MODEL 1
M C 0.68
G C 0.50
L H 0.48
K H 0.51
K H 0.57
F C 0.52
F C 0.58
K C 0.60
I C 0.64
K C 0.78
P C 0.77
P C 0.51
E H 0.53
E C 0.52
A C 0.75
T C 0.83
P C 0.50
E H 0.52
Q C 0.47
N C 0.60
K H 0.54
D H 0.52
T H 0.59
L H 0.60
M H 0.58
E H 0.57
L C 0.47
G C 0.70
I C 0.59
S E 0.44
V E 0.40
K C 0.48
N C 0.66
P H 0.66
S H 0.80
K H 0.85
K H 0.86
R H 0.89
K H 0.92
E H 0.92
K H 0.91
F H 0.92
A H 0.92
A H 0.90
Y H 0.73
G C 0.51
K H 0.54
F H 0.56
A C 0.50
N C 0.69
D C 0.71
K C 0.58
A C 0.65
E C 0.70
D C 0.79
K C 0.66
V C 0.59
Y C 0.54
A C 0.70
P C 0.85
P C 0.83
G C 0.83
Y C 0.59
E H 0.47
Q H 0.55
Y H 0.54
A C 0.47
R C 0.71
P C 0.69
Q H 0.87
D H 0.88
E H 0.88
L H 0.83
E H 0.76
D H 0.66
L C 0.48
N C 0.77
A C 0.85
S C 0.88
P C 0.60
L C 0.55
D C 0.60
A C 0.62
N C 0.73
A C 0.80
N C 0.80
E C 0.69
A C 0.66
T C 0.65
A C 0.70
G C 0.77
S C 0.79
N C 0.77
R C 0.77
G C 0.79
S C 0.73
S C 0.62
G H 0.48
T H 0.59
Q H 0.65
D H 0.58
L H 0.49
G C 0.66
N C 0.69
G C 0.65
A C 0.54
E H 0.45
S H 0.49
N C 0.57
S C 0.66
M C 0.66
Q C 0.68
D C 0.79
P C 0.54
Y C 0.47
A H 0.47
I H 0.38
E C 0.44
N C 0.56
D C 0.61
D C 0.61
Y C 0.64
R C 0.69
Y C 0.73
D C 0.74
D C 0.68
D C 0.59
P H 0.69
Y H 0.77
A H 0.79
R H 0.74
F H 0.65
Q H 0.54
A H 0.41
N C 0.54
K C 0.74
S C 0.78
N C 0.81
G C 0.82
R C 0.77
G C 0.58
S C 0.52
V E 0.57
N E 0.59
A E 0.54
A C 0.58
P C 0.62
Y C 0.72
G C 0.77
D C 0.74
Y C 0.66
G C 0.51
G E 0.67
G E 0.83
Y E 0.81
N E 0.72
G E 0.56
T E 0.49
S E 0.65
L E 0.71
N E 0.65
S C 0.48
Y C 0.64
N C 0.75
N C 0.78
D C 0.81
G C 0.83
P C 0.76
Y C 0.72
S C 0.73
N C 0.70
Q C 0.68
N C 0.71
T C 0.75
S C 0.77
N C 0.77
S C 0.65
W C 0.50
V C 0.52
N C 0.61
A C 0.67
N C 0.77
G C 0.82
R C 0.74
N C 0.68
S C 0.45
L E 0.63
N E 0.71
H E 0.72
S E 0.68
N E 0.55
S C 0.49
T C 0.51
L E 0.57
N E 0.67
V E 0.60
G C 0.69
P C 0.77
S C 0.74
R C 0.58
Q C 0.53
T C 0.58
R C 0.74
Q C 0.82
P C 0.84
P C 0.83
V C 0.72
S C 0.79
T C 0.85
S C 0.83
T C 0.83
N C 0.81
S C 0.64
L C 0.51
S C 0.57
L C 0.46
D H 0.46
Q C 0.49
R C 0.64
S C 0.75
P C 0.74
L C 0.78
A C 0.74
N C 0.68
P H 0.49
M H 0.56
Q H 0.59
E H 0.57
K C 0.63
R C 0.72
N C 0.73
P C 0.50
Y H 0.60
A H 0.66
D H 0.63
M H 0.56
N H 0.44
S C 0.46
Y C 0.50
G C 0.63
G C 0.64
A C 0.54
Y C 0.49
D C 0.48
S C 0.47
N H 0.46
T C 0.55
N C 0.64
R C 0.69
S C 0.69
S C 0.78
G C 0.85
T C 0.75
R C 0.70
Q C 0.68
G C 0.76
S C 0.70
S C 0.56
K C 0.50
N C 0.58
A C 0.68
N C 0.81
P C 0.67
Y C 0.60
A C 0.52
S C 0.46
M H 0.48
A C 0.50
N C 0.57
D C 0.73
S C 0.54
Y C 0.62
S C 0.56
N C 0.71
G C 0.70
N C 0.80
L C 0.66
N C 0.73
R C 0.66
S C 0.64
A C 0.64
N C 0.75
P C 0.73
Y C 0.73
S C 0.72
S C 0.58
R E 0.59
S E 0.74
V E 0.73
R E 0.58
Q C 0.55
P C 0.61
Q C 0.52
S C 0.58
Q C 0.72
Q C 0.82
A C 0.82
P C 0.77
M C 0.55
T C 0.55
Y C 0.57
T C 0.73
P C 0.59
S C 0.53
F H 0.52
I C 0.48
A C 0.63
S C 0.80
D H 0.64
E H 0.76
A H 0.78
A H 0.76
R H 0.69
N C 0.50
S C 0.72
E C 0.48
V H 0.49
D C 0.48
L H 0.51
N C 0.60
E C 0.73
E C 0.84
P C 0.81
R C 0.80
T C 0.73
G C 0.56
E E 0.64
F E 0.64
D C 0.62
F H 0.57
E H 0.61
E H 0.65
V H 0.50
Y C 0.52
A C 0.62
D C 0.73
K C 0.68
S C 0.60
A H 0.73
E H 0.70
N H 0.67
R H 0.68
A H 0.62
A H 0.53
L C 0.52
D C 0.62
E C 0.76
P C 0.83
D C 0.80
L C 0.73
N C 0.70
A C 0.55
V E 0.56
M E 0.55
T C 0.52
N C 0.73
E C 0.60
D C 0.58
S C 0.54
I C 0.53
D C 0.52
L C 0.61
N C 0.72
A C 0.48
S C 0.52
E C 0.49
V C 0.54
D C 0.63
H C 0.53
S C 0.53
S C 0.50
R H 0.54
Q H 0.66
Q H 0.65
Q H 0.66
Q H 0.54
Q C 0.52
Q C 0.55
W C 0.62
F C 0.63
M C 0.48
D C 0.48
E H 0.49
Q C 0.48
Q H 0.54
Q H 0.52
Q H 0.45
Q C 0.43
Q H 0.37
H H 0.35
F E 0.40
N C 0.54
A C 0.64
T C 0.75
N C 0.79
N C 0.85
Q C 0.78
Y C 0.71
G C 0.71
D C 0.78
Q C 0.71
R C 0.81
G C 0.83
Y C 0.75
K C 0.66
T C 0.63
F C 0.50
E C 0.43
E E 0.40
I C 0.41
Q C 0.48
K C 0.55
E H 0.63
E H 0.64
E H 0.67
A H 0.59
R C 0.53
Q C 0.53
Q C 0.56
Q H 0.54
E H 0.82
E H 0.86
D H 0.89
E H 0.93
A H 0.94
V H 0.94
D H 0.94
E H 0.93
I H 0.93
K H 0.88
Q H 0.86
E H 0.81
I H 0.72
K H 0.64
F H 0.58
T H 0.54
K H 0.52
Q H 0.62
S H 0.59
S H 0.59
V H 0.85
A H 0.90
S H 0.91
T H 0.94
R H 0.96
N H 0.96
T H 0.96
L H 0.96
K H 0.95
M H 0.94
A H 0.94
Q H 0.94
D H 0.92
A H 0.93
E H 0.94
R H 0.93
A H 0.87
G H 0.77
M H 0.90
N H 0.92
T H 0.94
L H 0.95
G H 0.94
M H 0.92
L H 0.88
G H 0.88
H H 0.84
Q H 0.84
S H 0.90
E H 0.92
Q H 0.93
L H 0.92
N H 0.91
N H 0.88
V H 0.87
E H 0.87
G H 0.79
N H 0.71
L H 0.62
D H 0.55
L H 0.70
M H 0.67
K H 0.59
V H 0.62
Q H 0.55
N H 0.69
K H 0.75
V H 0.87
A H 0.91
D H 0.94
E H 0.93
K H 0.90
V H 0.89
A H 0.86
E H 0.80
L H 0.75
K H 0.75
K H 0.65
L H 0.55
N C 0.51
R C 0.53
S C 0.46
I C 0.38
L E 0.46
A E 0.49
V E 0.55
H E 0.59
V E 0.49
S C 0.60
N C 0.75
P C 0.76
F C 0.77
N C 0.79
S C 0.79
K C 0.78
R C 0.76
R C 0.74
R C 0.63
R C 0.58
E C 0.49
R C 0.49
E H 0.50
E H 0.61
Q H 0.70
L H 0.70
K H 0.69
N H 0.62
R H 0.53
K H 0.53
I H 0.51
E H 0.60
E H 0.60
K H 0.55
L C 0.55
M C 0.64
R H 0.54
E C 0.50
Q C 0.56
T C 0.68
S C 0.69
Q C 0.64
Q C 0.54
L C 0.57
S C 0.63
Q C 0.70
S C 0.70
T C 0.53
Q H 0.52
R H 0.58
I H 0.64
E H 0.66
G H 0.67
A H 0.61
M H 0.54
N C 0.52
A C 0.61
N C 0.75
N C 0.77
N C 0.73
I C 0.66
S C 0.67
E C 0.57
V C 0.58
R C 0.61
E C 0.64
R C 0.65
Y C 0.62
Q C 0.66
R C 0.67
K C 0.57
N C 0.45
V H 0.60
L H 0.72
E H 0.76
K H 0.80
A H 0.74
K H 0.72
R H 0.71
Y H 0.62
Q H 0.47
F C 0.50
E C 0.56
N C 0.73
D C 0.83
E H 0.62
E H 0.63
D H 0.72
D H 0.81
E H 0.89
M H 0.91
E H 0.93
L H 0.94
E H 0.92
I H 0.92
D H 0.89
R H 0.81
N H 0.69
L H 0.91
D H 0.94
Q H 0.94
I H 0.95
Q H 0.95
Q H 0.95
V H 0.95
S H 0.94
N H 0.92
R H 0.92
L H 0.95
K H 0.96
K H 0.96
M H 0.95
A H 0.95
L H 0.94
T H 0.91
T H 0.80
G H 0.78
K H 0.88
E H 0.93
L H 0.94
D H 0.95
S H 0.93
Q H 0.94
Q H 0.94
K H 0.93
R H 0.90
L H 0.88
N H 0.79
N H 0.74
I H 0.77
E H 0.80
E H 0.85
S H 0.86
T H 0.82
D H 0.77
D H 0.74
L H 0.68
D H 0.60
I H 0.67
N H 0.70
L H 0.83
H H 0.85
M H 0.90
N H 0.91
T H 0.92
N H 0.92
R H 0.92
L H 0.92
A H 0.90
G H 0.76
I H 0.57
R C 0.80
END