PFRMAT SS
TARGET YGR023W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR023W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR023W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR023W.t2k.str2.rdb  (weight 1.54758)
METHOD YGR023W.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 YGR023W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR023W
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 YGR023W.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 2
METHOD
METHOD ============================================
METHOD Comments from YGR023W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR023W
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 YGR023W.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 2
METHOD
METHOD ============================================
METHOD Comments from YGR023W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR023W
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 YGR023W.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 2
METHOD
METHOD ============================================
METHOD Comments from YGR023W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR023W
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 YGR023W.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 2
METHOD
METHOD ============================================
MODEL 1
M C 0.85
A C 0.73
S C 0.73
C C 0.75
N C 0.81
P C 0.69
T C 0.65
R C 0.64
K C 0.62
K C 0.59
S C 0.64
S C 0.62
A H 0.52
S H 0.53
S H 0.63
L H 0.79
S H 0.84
M H 0.89
W H 0.92
R H 0.93
T H 0.93
I H 0.93
L H 0.93
M H 0.90
A H 0.87
L H 0.80
T H 0.69
T H 0.51
L C 0.58
P C 0.60
L H 0.47
S H 0.47
V H 0.43
L C 0.38
S C 0.45
Q C 0.43
E C 0.42
L E 0.42
V C 0.52
P C 0.64
A C 0.69
N C 0.77
S C 0.76
T C 0.71
T C 0.68
S C 0.71
S C 0.71
T C 0.72
A C 0.76
P C 0.71
S C 0.61
I C 0.49
T C 0.46
S C 0.42
L H 0.42
S H 0.42
A H 0.45
V H 0.40
E H 0.37
S C 0.36
F C 0.44
T C 0.52
S C 0.59
S C 0.66
T C 0.69
D C 0.72
A C 0.64
T C 0.63
S C 0.61
S C 0.58
A C 0.54
S C 0.57
L C 0.62
S C 0.70
T C 0.74
P C 0.69
S C 0.57
I E 0.45
A E 0.50
S E 0.63
V E 0.68
S E 0.67
F E 0.61
T E 0.46
S C 0.55
F C 0.69
P C 0.73
Q C 0.72
S C 0.67
S C 0.63
S C 0.54
L E 0.41
L E 0.47
T E 0.48
L E 0.36
S C 0.38
S H 0.45
T H 0.44
L H 0.47
S H 0.48
S H 0.52
E H 0.46
L C 0.49
S C 0.60
S C 0.59
S C 0.61
S C 0.58
M C 0.48
Q E 0.56
V E 0.60
S C 0.49
S C 0.61
S C 0.70
S C 0.70
T C 0.70
S C 0.70
S C 0.71
S C 0.71
S C 0.67
S C 0.61
E C 0.48
V E 0.48
T C 0.49
S C 0.58
S C 0.68
S C 0.72
S C 0.73
S C 0.69
S C 0.68
S C 0.64
I C 0.60
S C 0.74
P C 0.71
S C 0.74
S C 0.75
S C 0.75
S C 0.69
S C 0.62
T E 0.53
I E 0.70
I E 0.69
S E 0.53
S C 0.61
S C 0.70
S C 0.72
S C 0.73
L C 0.76
P C 0.72
T E 0.48
F E 0.68
T E 0.76
V E 0.76
A E 0.65
S E 0.49
T C 0.57
S C 0.60
S C 0.52
T E 0.43
V E 0.48
A E 0.43
S C 0.43
S C 0.47
T C 0.44
L C 0.44
S C 0.52
T C 0.56
S C 0.63
S C 0.59
S E 0.55
L E 0.79
V E 0.86
I E 0.84
S E 0.74
T E 0.51
S C 0.65
S C 0.69
S C 0.65
T E 0.50
F E 0.69
T E 0.70
F E 0.63
S C 0.53
S C 0.64
E C 0.68
S C 0.68
S C 0.62
S C 0.56
S C 0.42
L E 0.51
I E 0.57
S E 0.51
S C 0.49
S C 0.54
I C 0.54
S C 0.61
T C 0.62
S C 0.62
V C 0.59
S C 0.62
T C 0.60
S C 0.56
S E 0.54
V E 0.66
Y E 0.71
V E 0.60
P C 0.58
S C 0.71
S C 0.76
S C 0.76
T C 0.77
S C 0.79
S C 0.82
P C 0.83
P C 0.71
S C 0.68
S C 0.65
S C 0.61
S C 0.57
E C 0.53
L C 0.54
T C 0.60
S C 0.65
S C 0.68
S C 0.66
Y C 0.62
S C 0.62
S C 0.56
S C 0.58
S C 0.58
S C 0.57
S C 0.53
S C 0.46
T E 0.57
L E 0.69
F E 0.72
S E 0.67
Y E 0.57
S C 0.57
S C 0.69
S C 0.75
F C 0.72
S C 0.72
S C 0.71
S C 0.73
S C 0.72
S C 0.71
S C 0.71
S C 0.70
S C 0.70
S C 0.73
S C 0.74
S C 0.75
S C 0.74
S C 0.73
S C 0.72
S C 0.72
S C 0.71
S C 0.69
S C 0.66
S C 0.64
S C 0.60
S C 0.62
S C 0.61
S C 0.58
Y C 0.48
F E 0.52
T E 0.49
L C 0.50
S C 0.58
T C 0.63
S C 0.69
S C 0.70
S C 0.70
S C 0.67
S C 0.59
I C 0.50
Y C 0.50
S C 0.58
S C 0.67
S C 0.72
S C 0.73
Y C 0.74
P C 0.71
S C 0.64
F C 0.60
S C 0.65
S C 0.68
S C 0.76
S C 0.77
S C 0.80
S C 0.82
N C 0.86
P C 0.81
T C 0.73
S C 0.59
S C 0.47
I E 0.54
T E 0.47
S C 0.55
T C 0.66
S C 0.72
A C 0.70
S C 0.71
S C 0.72
S C 0.70
I C 0.67
T C 0.78
P C 0.67
A C 0.60
S C 0.55
E C 0.50
Y C 0.46
S C 0.49
N C 0.56
L H 0.47
A H 0.47
K H 0.46
T H 0.45
I H 0.50
T H 0.52
S H 0.50
I H 0.48
I H 0.38
E C 0.57
G C 0.76
Q C 0.56
T E 0.64
I E 0.67
L E 0.67
S E 0.52
N C 0.53
Y E 0.48
Y E 0.71
T E 0.79
T E 0.85
I E 0.84
T E 0.79
Y E 0.68
S C 0.60
P C 0.64
T C 0.69
A C 0.63
S C 0.65
A C 0.63
S C 0.70
S C 0.75
G C 0.77
K C 0.75
N C 0.75
S C 0.71
H C 0.69
H C 0.66
S C 0.71
G C 0.73
L C 0.66
S C 0.64
K C 0.55
K C 0.57
N C 0.60
R C 0.60
N C 0.51
I E 0.76
I E 0.83
I E 0.77
G E 0.68
C E 0.60
V E 0.50
V C 0.44
G C 0.59
I C 0.52
G C 0.55
A H 0.83
P H 0.94
L H 0.96
I H 0.96
L H 0.96
I H 0.96
L H 0.96
L H 0.96
I H 0.96
L H 0.95
I H 0.94
Y H 0.92
M H 0.88
F H 0.74
C H 0.51
V C 0.61
Q C 0.78
P C 0.75
K C 0.76
K C 0.70
T C 0.73
D C 0.61
F E 0.54
I E 0.70
D C 0.71
S C 0.84
D C 0.92
G C 0.89
K C 0.63
I E 0.87
V E 0.85
T E 0.85
A E 0.77
Y E 0.68
R E 0.54
S C 0.52
N C 0.65
I H 0.49
F H 0.69
T H 0.83
K H 0.91
I H 0.92
W H 0.92
Y H 0.92
F H 0.92
L H 0.87
L H 0.62
G C 0.71
K C 0.67
K C 0.52
I C 0.62
G C 0.77
E C 0.71
T C 0.62
E C 0.59
R C 0.57
F C 0.59
S C 0.70
S C 0.77
D C 0.82
S C 0.84
P C 0.75
I C 0.73
G C 0.79
S C 0.73
N C 0.64
N C 0.59
I C 0.54
Q C 0.54
N C 0.56
F C 0.64
G C 0.75
D C 0.76
I C 0.74
D C 0.84
P H 0.72
E H 0.79
D H 0.81
I H 0.70
L H 0.50
N C 0.66
N C 0.81
D C 0.84
N C 0.85
P C 0.78
Y C 0.75
T C 0.79
P C 0.70
K C 0.64
H C 0.63
T C 0.67
N C 0.71
V C 0.70
E C 0.76
G C 0.78
Y C 0.72
D C 0.74
D C 0.72
D C 0.74
D C 0.63
D C 0.60
D C 0.63
D C 0.59
A H 0.58
N H 0.56
D H 0.60
E H 0.54
N C 0.52
L C 0.49
S H 0.49
S H 0.51
N C 0.51
F C 0.52
H C 0.54
N C 0.50
R C 0.50
G C 0.55
I C 0.60
D C 0.67
D C 0.69
Q C 0.71
Y C 0.72
S C 0.78
P C 0.70
T C 0.68
K C 0.65
S C 0.64
A C 0.61
S C 0.62
Y C 0.58
S C 0.58
M C 0.63
S C 0.71
N C 0.74
S C 0.74
N C 0.77
S C 0.72
Q C 0.66
D C 0.64
Y C 0.65
N C 0.71
D C 0.70
A C 0.51
D C 0.48
E H 0.50
V H 0.46
M C 0.54
H C 0.70
D C 0.75
E C 0.66
N C 0.59
I C 0.55
H C 0.53
R C 0.46
V C 0.46
Y C 0.56
D C 0.71
D C 0.56
S C 0.55
E H 0.57
A H 0.62
S H 0.60
I H 0.59
D H 0.56
E H 0.63
N H 0.58
Y H 0.47
Y C 0.47
T C 0.60
K C 0.74
P C 0.75
N C 0.78
N C 0.79
G C 0.76
L C 0.67
N C 0.71
I C 0.58
T C 0.64
N C 0.71
Y C 0.90
END