PFRMAT SS
TARGET A
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR027W-A.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR027W-A.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR027W-A.t2k.str2.rdb  (weight 1.54758)
METHOD YGR027W-A.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 YGR027W-A.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR027W-A
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 YGR027W-A.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 7
METHOD
METHOD ============================================
METHOD Comments from YGR027W-A.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR027W-A
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 YGR027W-A.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 7
METHOD
METHOD ============================================
METHOD Comments from YGR027W-A.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR027W-A
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 YGR027W-A.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 7
METHOD
METHOD ============================================
METHOD Comments from YGR027W-A.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR027W-A
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 YGR027W-A.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 7
METHOD
METHOD ============================================
MODEL 1
M C 0.64
E H 0.46
S H 0.48
Q H 0.51
Q H 0.48
L H 0.46
S C 0.47
Q C 0.57
H C 0.76
S C 0.85
H C 0.78
I C 0.68
S C 0.64
H C 0.68
G C 0.67
S C 0.55
A E 0.48
C E 0.67
A E 0.74
S E 0.79
V E 0.69
T E 0.50
S C 0.60
K C 0.58
E C 0.55
V C 0.64
H C 0.72
T C 0.75
N C 0.78
Q C 0.78
D C 0.84
P C 0.70
L C 0.61
D C 0.48
V C 0.50
S C 0.58
A C 0.48
S C 0.56
K C 0.57
T C 0.50
E H 0.49
E H 0.51
C H 0.49
E C 0.46
K C 0.55
A C 0.67
S C 0.73
T C 0.71
K C 0.62
A C 0.67
N C 0.75
S C 0.77
Q C 0.75
Q C 0.77
T C 0.80
T C 0.80
T C 0.85
P C 0.80
A C 0.74
S C 0.67
S C 0.65
A C 0.61
V C 0.62
P C 0.75
E C 0.73
N C 0.79
P C 0.82
H C 0.81
H C 0.69
A C 0.75
S C 0.80
P C 0.70
Q C 0.68
T C 0.60
A C 0.66
Q C 0.75
S C 0.87
H C 0.86
S C 0.84
P C 0.83
Q C 0.81
N C 0.81
G C 0.85
P C 0.71
Y C 0.56
P C 0.48
Q C 0.48
Q C 0.55
C C 0.66
M C 0.72
M C 0.73
T C 0.82
Q C 0.71
N C 0.70
Q C 0.64
A C 0.63
N C 0.71
P C 0.67
S C 0.74
G C 0.73
W C 0.63
S C 0.51
F C 0.56
Y C 0.70
G C 0.81
H C 0.84
P C 0.71
S C 0.68
M C 0.62
I C 0.73
P C 0.82
Y C 0.81
T C 0.86
P C 0.57
Y C 0.54
Q C 0.53
M C 0.66
S C 0.80
P C 0.75
M C 0.66
Y C 0.62
F C 0.73
P C 0.86
P C 0.85
G C 0.85
P C 0.77
Q C 0.78
S C 0.78
Q C 0.78
F C 0.79
P C 0.78
Q C 0.61
Y C 0.59
P C 0.68
S C 0.73
S C 0.72
V C 0.77
G C 0.81
T C 0.77
P C 0.76
L C 0.72
S C 0.70
T C 0.77
P C 0.75
S C 0.80
P C 0.80
E C 0.81
S C 0.77
G C 0.77
N C 0.75
T C 0.75
F C 0.77
T C 0.78
D C 0.78
S C 0.75
S C 0.64
S C 0.63
A C 0.67
D C 0.74
S C 0.65
D C 0.70
M C 0.61
T C 0.64
S C 0.69
T C 0.74
K C 0.77
K C 0.72
Y C 0.64
V C 0.65
R C 0.79
P C 0.82
P C 0.82
P C 0.74
M C 0.57
L C 0.65
T C 0.75
S C 0.87
P C 0.63
N C 0.62
D C 0.58
F H 0.71
P H 0.90
N H 0.93
W H 0.95
V H 0.96
K H 0.96
T H 0.96
Y H 0.96
I H 0.96
K H 0.96
F H 0.95
L H 0.93
Q H 0.84
N H 0.65
S C 0.62
N C 0.80
L C 0.67
G C 0.56
G C 0.55
I C 0.61
I C 0.66
P C 0.75
T C 0.83
V C 0.81
N C 0.88
G C 0.90
K C 0.77
P C 0.58
V C 0.69
R C 0.70
Q C 0.75
I C 0.80
T C 0.86
D H 0.83
D H 0.89
E H 0.93
L H 0.95
T H 0.94
F H 0.94
L H 0.95
Y H 0.94
N H 0.93
T H 0.93
F H 0.91
Q H 0.89
I H 0.81
F H 0.65
A C 0.72
P C 0.78
S H 0.66
Q H 0.68
F H 0.62
L C 0.59
P H 0.79
T H 0.89
W H 0.90
V H 0.91
K H 0.90
D H 0.85
I H 0.76
L H 0.63
S C 0.54
V C 0.61
D C 0.67
Y H 0.91
T H 0.95
D H 0.95
I H 0.96
M H 0.96
K H 0.96
I H 0.95
L H 0.95
S H 0.94
K H 0.92
S H 0.91
I H 0.89
E H 0.86
K H 0.81
M H 0.67
Q H 0.50
S C 0.62
D C 0.72
T C 0.75
Q C 0.74
E H 0.67
A H 0.84
N H 0.88
D H 0.90
I H 0.92
V H 0.90
T H 0.89
L H 0.88
A H 0.78
N C 0.48
L C 0.58
Q C 0.54
Y C 0.60
N C 0.80
G C 0.83
S C 0.75
T C 0.70
P C 0.82
A H 0.68
D H 0.87
A H 0.90
F H 0.93
E H 0.95
T H 0.95
K H 0.95
V H 0.95
T H 0.95
N H 0.94
I H 0.95
I H 0.95
D H 0.94
R H 0.93
L H 0.91
N H 0.86
N H 0.72
N C 0.64
G C 0.92
I C 0.88
H C 0.82
I H 0.51
N H 0.54
N H 0.70
K H 0.80
V H 0.79
A H 0.86
C H 0.88
Q H 0.90
L H 0.90
I H 0.89
M H 0.85
R H 0.69
G C 0.58
L C 0.81
S C 0.81
G C 0.77
E C 0.67
Y C 0.49
K E 0.48
F E 0.48
L C 0.36
R C 0.36
Y H 0.50
T H 0.42
R C 0.41
H C 0.48
R C 0.53
H C 0.58
L C 0.60
N C 0.66
M C 0.50
T C 0.45
V H 0.78
A H 0.89
E H 0.89
L H 0.89
F H 0.91
L H 0.91
D H 0.92
I H 0.94
H H 0.94
A H 0.92
I H 0.90
Y H 0.87
E H 0.88
E H 0.88
Q H 0.85
Q H 0.81
G H 0.78
S H 0.64
R C 0.48
N C 0.67
S C 0.79
K C 0.83
P C 0.79
N C 0.73
Y C 0.72
R C 0.76
R C 0.77
N C 0.83
L C 0.68
S C 0.67
D C 0.62
E C 0.66
K C 0.71
N C 0.71
D C 0.70
S C 0.71
R C 0.71
S C 0.70
Y C 0.75
T C 0.76
N C 0.78
T C 0.80
T C 0.81
K C 0.82
P C 0.75
K C 0.51
V E 0.62
I E 0.62
A E 0.61
R E 0.49
N C 0.66
P C 0.74
Q C 0.75
K C 0.77
T C 0.81
N C 0.84
N C 0.86
S C 0.81
K C 0.72
S C 0.56
K H 0.39
T E 0.39
A E 0.44
R E 0.49
A E 0.42
H C 0.47
N C 0.55
V C 0.55
S C 0.55
T C 0.66
S C 0.74
N C 0.80
N C 0.83
S C 0.83
P C 0.80
S C 0.82
T C 0.77
D C 0.73
N C 0.70
D C 0.66
S C 0.59
I C 0.58
S C 0.70
K C 0.77
S C 0.79
T C 0.79
T C 0.78
E C 0.75
P C 0.58
I E 0.63
Q E 0.68
L C 0.47
N C 0.76
N C 0.84
K C 0.76
H C 0.68
D C 0.49
L C 0.45
H C 0.48
L C 0.54
R C 0.76
P C 0.70
G C 0.75
T C 0.74
Y C 0.91
END