PFRMAT SS
TARGET YGR212W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR212W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR212W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR212W.t2k.str2.rdb  (weight 1.54758)
METHOD YGR212W.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 YGR212W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR212W
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 YGR212W.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 1
METHOD
METHOD ============================================
METHOD Comments from YGR212W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR212W
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 YGR212W.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 1
METHOD
METHOD ============================================
METHOD Comments from YGR212W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR212W
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 YGR212W.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 1
METHOD
METHOD ============================================
METHOD Comments from YGR212W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR212W
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 YGR212W.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 1
METHOD
METHOD ============================================
MODEL 1
M C 0.83
N C 0.65
L C 0.53
K C 0.46
L H 0.60
S H 0.64
A H 0.66
I H 0.70
E H 0.70
S H 0.70
Y H 0.67
F H 0.57
F H 0.51
H H 0.43
R H 0.49
S C 0.48
R C 0.48
L C 0.51
N C 0.57
L C 0.48
H C 0.48
S C 0.42
C E 0.46
F E 0.55
Y E 0.62
V E 0.54
G E 0.56
I E 0.61
K E 0.59
L C 0.43
N C 0.57
E C 0.63
L C 0.72
P C 0.72
K C 0.60
K H 0.56
S H 0.64
Q H 0.68
L H 0.73
I H 0.77
A H 0.75
A H 0.68
L H 0.58
K H 0.49
Y E 0.42
T E 0.55
V E 0.62
I E 0.55
Q E 0.43
H C 0.41
E C 0.44
R C 0.40
L C 0.37
T E 0.40
C H 0.36
N H 0.39
V H 0.45
F H 0.47
Y H 0.63
D H 0.70
E H 0.75
L H 0.72
K H 0.64
K H 0.67
E H 0.69
N H 0.63
F H 0.69
L H 0.78
Q H 0.78
N H 0.73
I H 0.67
L H 0.60
E H 0.47
P H 0.55
L H 0.51
K H 0.47
F H 0.49
C H 0.47
D H 0.45
L H 0.52
V H 0.46
E H 0.42
Y H 0.40
R C 0.46
H C 0.50
D C 0.55
W H 0.57
D H 0.57
Q H 0.58
L C 0.49
G C 0.64
E C 0.50
T H 0.48
E H 0.48
I H 0.56
N H 0.56
H H 0.58
I H 0.57
F H 0.49
Q H 0.43
R H 0.39
Y C 0.45
N C 0.56
F C 0.55
S C 0.57
Y C 0.63
N C 0.75
E C 0.79
N C 0.83
K C 0.78
P C 0.63
L E 0.53
W E 0.66
K E 0.74
I E 0.83
L E 0.85
I E 0.82
L E 0.58
P C 0.68
N C 0.80
Q C 0.70
N C 0.67
Q C 0.45
M E 0.63
L E 0.73
L E 0.77
L E 0.68
T E 0.51
D C 0.41
H E 0.44
V E 0.60
L E 0.52
M C 0.43
D C 0.63
G C 0.69
M C 0.53
S C 0.39
A H 0.50
I H 0.58
H H 0.61
V H 0.71
W H 0.78
E H 0.82
T H 0.81
F H 0.78
M H 0.74
E H 0.62
G C 0.55
L C 0.59
Q C 0.56
M C 0.58
Q C 0.68
Q C 0.71
P C 0.63
V C 0.54
E E 0.51
I C 0.48
D C 0.55
E C 0.50
T C 0.43
I E 0.44
Y C 0.53
S C 0.68
P C 0.63
S C 0.64
L C 0.65
N C 0.72
S C 0.65
S C 0.60
T C 0.48
E H 0.44
K H 0.44
I H 0.39
M C 0.36
S C 0.46
A C 0.59
P C 0.62
L C 0.57
Y C 0.63
G C 0.75
D C 0.77
W C 0.77
P C 0.78
I C 0.75
P C 0.72
W C 0.55
N H 0.51
W H 0.76
H H 0.82
I H 0.85
V H 0.88
R H 0.90
Q H 0.89
L H 0.88
V H 0.84
S H 0.80
R H 0.75
L H 0.66
H H 0.56
Y H 0.48
W C 0.44
F C 0.58
P C 0.54
Q C 0.44
T H 0.35
V E 0.43
V E 0.41
K C 0.45
N C 0.63
N C 0.68
R C 0.58
N C 0.50
L E 0.38
I E 0.50
Q E 0.47
F E 0.38
A C 0.41
N C 0.54
Y C 0.60
S C 0.62
F C 0.70
P C 0.62
K H 0.57
D H 0.60
L H 0.58
L C 0.47
D C 0.63
D C 0.75
K C 0.81
P C 0.80
S C 0.79
D C 0.80
G C 0.80
T C 0.67
Q C 0.48
K E 0.55
Y E 0.62
K E 0.69
V E 0.66
K E 0.53
N C 0.53
T C 0.63
N C 0.67
H C 0.57
Q E 0.48
W E 0.60
E E 0.66
F E 0.65
R E 0.59
L C 0.50
S C 0.76
P C 0.56
T C 0.52
H C 0.47
L H 0.72
N H 0.78
D H 0.82
I H 0.86
L H 0.85
Q H 0.83
E H 0.78
C H 0.66
K H 0.53
A C 0.51
N C 0.67
N C 0.70
T C 0.57
S C 0.46
L H 0.61
T H 0.66
S H 0.67
L H 0.67
L H 0.62
G H 0.52
A H 0.54
L H 0.49
V H 0.44
C H 0.41
T H 0.43
S H 0.46
F H 0.72
E H 0.73
K H 0.72
I H 0.71
A H 0.65
A H 0.63
H H 0.52
E C 0.45
Y C 0.52
T C 0.62
G C 0.71
S C 0.57
F E 0.47
L E 0.56
K E 0.62
I E 0.53
E E 0.45
L C 0.59
P C 0.61
M C 0.56
N C 0.57
I C 0.59
R C 0.64
K C 0.66
P C 0.53
F H 0.49
E H 0.52
R H 0.48
V H 0.43
L C 0.37
K C 0.50
L C 0.72
P C 0.80
S C 0.76
D C 0.70
D C 0.67
K C 0.55
L C 0.47
A C 0.45
V C 0.41
G C 0.49
N E 0.40
F E 0.65
I E 0.72
A E 0.75
V E 0.73
I E 0.69
E E 0.63
F E 0.48
N C 0.38
H H 0.41
K H 0.46
L H 0.50
H C 0.45
Q C 0.49
N C 0.55
R C 0.58
G C 0.61
I H 0.49
W H 0.61
D H 0.66
I H 0.79
A H 0.84
S H 0.84
Q H 0.84
I H 0.85
Q H 0.86
R H 0.85
A H 0.82
I H 0.72
R H 0.59
S C 0.47
S C 0.57
S C 0.55
E H 0.59
D H 0.62
K H 0.65
I H 0.67
I H 0.63
D H 0.60
K H 0.59
V H 0.52
N C 0.43
E H 0.53
V H 0.47
K H 0.41
L H 0.48
L H 0.49
E H 0.43
V H 0.43
I H 0.38
S C 0.39
S H 0.47
Q H 0.53
Q H 0.51
Y H 0.46
I H 0.47
E H 0.46
D C 0.43
K C 0.45
I C 0.40
S C 0.46
L C 0.57
N C 0.72
N C 0.81
G C 0.85
P C 0.78
S C 0.71
S C 0.64
T C 0.51
F E 0.58
E E 0.67
V E 0.65
T E 0.51
N C 0.46
L C 0.54
G C 0.56
F C 0.43
Q C 0.34
T C 0.38
F H 0.49
K H 0.55
D H 0.59
A H 0.56
C C 0.53
N C 0.68
T C 0.69
S C 0.72
L C 0.70
P C 0.60
F E 0.61
Y E 0.77
I E 0.81
V E 0.74
D E 0.61
A C 0.43
T C 0.48
F C 0.57
N C 0.71
E C 0.74
P C 0.68
Q C 0.67
G C 0.69
I C 0.52
S C 0.42
S E 0.47
I E 0.60
F E 0.67
S E 0.72
L E 0.72
S E 0.77
V E 0.82
I E 0.77
S E 0.66
T C 0.61
P C 0.80
G C 0.84
N C 0.81
G C 0.71
L E 0.55
H E 0.68
C E 0.74
C E 0.72
I E 0.65
S E 0.53
Y C 0.63
P C 0.64
N C 0.59
T C 0.47
L H 0.50
T H 0.57
K H 0.55
V H 0.50
L H 0.46
E C 0.48
P H 0.59
H H 0.64
W H 0.76
Q H 0.80
Y H 0.79
M H 0.80
K H 0.82
D H 0.78
Y H 0.74
L H 0.59
N C 0.51
L C 0.65
Y C 0.91
END