PFRMAT SS
TARGET YGR223C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR223C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR223C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR223C.t2k.str.rdb  (weight 1.53983)
METHOD YGR223C.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 YGR223C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR223C
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 YGR223C.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 290
METHOD
METHOD ============================================
METHOD Comments from YGR223C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR223C
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 YGR223C.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 290
METHOD
METHOD ============================================
METHOD Comments from YGR223C.t2k.str.rdb
METHOD ============================================
METHOD TARGET YGR223C
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.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 str )
METHOD The input amino acid frequencies were determined from
METHOD alignment YGR223C.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 290
METHOD
METHOD ============================================
METHOD Comments from YGR223C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR223C
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 YGR223C.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 290
METHOD
METHOD ============================================
MODEL 1
M C 0.90
D C 0.83
V C 0.81
R C 0.78
R C 0.69
P H 0.51
I H 0.59
R H 0.66
E H 0.64
A H 0.56
V H 0.51
N H 0.40
N C 0.53
R C 0.74
R C 0.74
K C 0.75
P C 0.81
K C 0.53
F E 0.79
L E 0.85
S E 0.91
V E 0.92
S E 0.91
F E 0.88
N C 0.64
Q C 0.87
D C 0.92
D C 0.88
S C 0.59
C E 0.89
F E 0.90
S E 0.92
V E 0.89
A E 0.82
L E 0.51
E C 0.79
N C 0.88
G C 0.79
F E 0.63
R E 0.86
I E 0.90
F E 0.86
N E 0.78
T C 0.56
D C 0.81
P C 0.83
L C 0.78
T C 0.52
S E 0.51
K E 0.51
L E 0.43
S E 0.38
K C 0.37
T C 0.41
F C 0.49
K C 0.54
E C 0.61
S C 0.65
A C 0.61
T C 0.52
N C 0.47
Q C 0.52
S C 0.63
R C 0.68
G C 0.72
T C 0.79
G C 0.57
I E 0.75
G E 0.83
Y E 0.90
T E 0.91
R E 0.91
M E 0.89
L E 0.51
Y C 0.85
R C 0.91
T C 0.89
N C 0.69
Y E 0.86
I E 0.91
A E 0.92
L E 0.89
V E 0.78
G E 0.49
G C 0.69
G C 0.78
K C 0.79
R C 0.77
P C 0.69
R C 0.67
H C 0.66
A C 0.73
L C 0.76
N C 0.77
K E 0.59
L E 0.80
I E 0.90
I E 0.91
W E 0.87
D E 0.83
D C 0.54
L C 0.80
L C 0.88
Q C 0.88
K E 0.63
E E 0.87
T E 0.89
I E 0.90
T E 0.90
L E 0.87
K E 0.72
F C 0.56
M C 0.70
S C 0.70
S C 0.53
I E 0.62
K E 0.66
D E 0.84
V E 0.90
F E 0.90
L E 0.86
S C 0.58
R C 0.86
I C 0.92
H C 0.80
I E 0.57
V E 0.89
V E 0.90
V E 0.88
L E 0.68
E C 0.81
N C 0.83
T E 0.69
I E 0.89
E E 0.91
I E 0.92
F E 0.89
Q E 0.80
F C 0.56
Q C 0.84
T C 0.87
N C 0.82
P E 0.51
Q E 0.72
R E 0.75
I E 0.77
C E 0.67
P E 0.67
I E 0.77
L E 0.80
D E 0.80
I E 0.79
P E 0.68
P E 0.67
N C 0.79
G C 0.87
S C 0.92
V C 0.88
D C 0.63
Y E 0.86
V E 0.89
V E 0.89
C E 0.81
S E 0.65
S C 0.66
K C 0.81
H C 0.85
L C 0.81
Q C 0.61
S E 0.56
Q E 0.67
A E 0.67
S E 0.59
Q E 0.56
S C 0.43
Q C 0.56
S C 0.73
K C 0.76
I C 0.61
L C 0.50
E E 0.58
I E 0.73
I E 0.79
A E 0.78
F E 0.65
P C 0.49
S C 0.67
N C 0.72
K C 0.76
C C 0.72
V C 0.78
G C 0.75
Q C 0.57
I E 0.74
Q E 0.88
V E 0.88
A E 0.81
D E 0.74
L C 0.50
S C 0.67
Q C 0.75
I C 0.80
K C 0.80
Y C 0.74
N C 0.67
S C 0.65
Q C 0.67
N C 0.69
P C 0.67
K C 0.64
E C 0.64
S C 0.69
A C 0.74
L C 0.73
L C 0.51
P E 0.65
T E 0.78
S E 0.82
I E 0.82
I E 0.77
K E 0.56
A C 0.61
H C 0.69
K C 0.76
N C 0.81
P C 0.57
I E 0.73
K E 0.82
L E 0.92
V E 0.92
R E 0.91
L E 0.88
N C 0.67
R C 0.87
Q C 0.93
G C 0.89
T C 0.62
M E 0.90
V E 0.91
A E 0.91
T E 0.88
C E 0.84
S E 0.49
V C 0.79
Q C 0.86
G C 0.82
T C 0.52
L E 0.85
I E 0.89
R E 0.91
I E 0.91
F E 0.89
S E 0.87
T C 0.50
H C 0.80
N C 0.90
G C 0.88
T E 0.60
L E 0.88
I E 0.88
K E 0.88
E E 0.87
F E 0.82
R E 0.65
R C 0.55
G C 0.69
V C 0.76
D C 0.82
K C 0.81
A C 0.79
D C 0.72
I E 0.63
Y E 0.77
E E 0.87
M E 0.91
S E 0.90
F E 0.87
S C 0.57
P C 0.87
N C 0.92
G C 0.87
S C 0.62
K E 0.89
L E 0.91
A E 0.92
V E 0.90
L E 0.86
S E 0.53
N C 0.82
K C 0.90
Q C 0.84
T E 0.75
L E 0.90
H E 0.92
I E 0.91
F E 0.88
Q E 0.86
I E 0.53
F C 0.70
E C 0.85
T C 0.87
T C 0.55
N E 0.72
T E 0.78
E E 0.73
T E 0.68
N E 0.59
T C 0.53
P C 0.68
D C 0.71
H C 0.69
S C 0.69
R C 0.57
A E 0.45
N E 0.52
G E 0.55
S E 0.59
S E 0.60
H E 0.56
P C 0.65
L C 0.73
K C 0.80
N C 0.77
Y C 0.67
I C 0.56
P C 0.54
K C 0.56
G C 0.55
L C 0.45
W E 0.51
R E 0.50
P C 0.44
K C 0.49
Y C 0.53
L C 0.60
D C 0.71
S C 0.73
V C 0.73
W C 0.68
S C 0.55
I E 0.52
C E 0.58
N E 0.63
A E 0.63
H E 0.58
L C 0.60
K C 0.74
N C 0.75
P C 0.66
I C 0.48
F H 0.39
D H 0.42
A H 0.42
H H 0.41
R C 0.45
N C 0.60
D C 0.69
N C 0.69
S C 0.64
G C 0.64
D C 0.52
V E 0.56
T E 0.63
H E 0.65
D E 0.65
N E 0.65
E E 0.64
F C 0.65
Y C 0.79
K C 0.86
D C 0.80
R E 0.55
C E 0.86
R E 0.87
I E 0.89
G E 0.83
W E 0.72
C C 0.51
Q C 0.75
D C 0.79
S C 0.65
N E 0.65
N E 0.80
R E 0.84
E E 0.82
Q E 0.75
D C 0.57
D C 0.76
S C 0.86
L C 0.82
V E 0.49
L E 0.82
V E 0.82
W E 0.82
Q E 0.74
N E 0.58
S C 0.63
G C 0.80
I C 0.76
W C 0.74
E C 0.75
K C 0.48
F E 0.79
V E 0.86
I E 0.90
L E 0.91
E E 0.90
K E 0.87
E C 0.54
Q C 0.86
Q C 0.92
D C 0.89
S C 0.62
S E 0.89
K E 0.92
T E 0.93
H E 0.91
Y E 0.88
S E 0.54
L C 0.82
N C 0.89
E C 0.83
S E 0.70
L E 0.90
R E 0.91
N E 0.91
E E 0.87
D E 0.84
T E 0.65
K C 0.63
S C 0.80
A C 0.81
G C 0.78
E C 0.74
P C 0.60
T E 0.55
R E 0.70
W E 0.68
E E 0.76
L E 0.70
V E 0.62
R E 0.40
E H 0.42
S H 0.43
W H 0.41
R C 0.51
E C 0.73
L C 0.91
END