PFRMAT SS
TARGET YGR013W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR013W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR013W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR013W.t2k.str2.rdb  (weight 1.54758)
METHOD YGR013W.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 YGR013W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR013W
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 YGR013W.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 YGR013W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR013W
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 YGR013W.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 YGR013W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR013W
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 YGR013W.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 YGR013W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR013W
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 YGR013W.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 0.88
R C 0.76
D C 0.60
I E 0.60
V E 0.77
F E 0.79
V E 0.63
S C 0.64
P C 0.58
Q C 0.47
L E 0.34
Y E 0.43
L E 0.40
S C 0.50
S C 0.58
Q C 0.57
E C 0.58
G C 0.65
W C 0.60
K C 0.56
S C 0.56
D C 0.57
S C 0.55
A C 0.52
K C 0.49
S C 0.55
G C 0.66
F C 0.50
I C 0.38
P H 0.40
I H 0.47
L H 0.46
K H 0.63
N H 0.63
D H 0.66
L H 0.78
Q H 0.80
R H 0.77
F H 0.76
Q H 0.80
D H 0.77
S H 0.77
L H 0.79
K H 0.78
H H 0.75
I H 0.71
V H 0.61
D H 0.51
A H 0.58
R H 0.49
N C 0.49
S C 0.51
L H 0.48
S H 0.48
E H 0.56
T H 0.53
L H 0.50
L H 0.40
N C 0.54
S C 0.69
N C 0.79
D C 0.80
D C 0.80
G C 0.77
S C 0.64
I C 0.51
H C 0.58
N C 0.67
S C 0.67
D C 0.66
Q C 0.65
N C 0.63
T C 0.64
G C 0.70
L C 0.68
N C 0.70
K C 0.58
D C 0.57
K C 0.47
E H 0.46
A H 0.43
S C 0.40
I C 0.41
A C 0.49
D C 0.61
N C 0.70
N C 0.71
S C 0.64
A C 0.54
N C 0.53
K C 0.49
C C 0.50
A C 0.52
T C 0.57
S C 0.58
S C 0.49
S H 0.55
R H 0.62
Y H 0.74
Q H 0.75
E H 0.75
L H 0.75
K H 0.72
Q H 0.67
F H 0.54
L C 0.53
P C 0.58
I C 0.53
S C 0.59
L C 0.53
D C 0.57
Q C 0.54
Q C 0.48
I E 0.49
H E 0.57
T E 0.70
V E 0.71
S E 0.68
L E 0.55
Q C 0.50
G C 0.59
V C 0.53
S C 0.53
S C 0.54
S C 0.54
F C 0.55
S C 0.57
R H 0.54
G H 0.56
Q H 0.64
I H 0.82
E H 0.86
S H 0.86
L H 0.86
L H 0.86
D H 0.83
H H 0.78
C H 0.73
L H 0.71
N H 0.62
L H 0.60
A H 0.50
L H 0.45
T C 0.42
E C 0.45
T C 0.52
Q C 0.57
S C 0.61
N C 0.61
S C 0.53
A C 0.41
L H 0.39
K H 0.37
V H 0.47
E H 0.50
A H 0.56
W H 0.58
S H 0.56
S H 0.55
F H 0.57
S H 0.59
S H 0.58
F H 0.53
L C 0.49
D C 0.62
T C 0.53
Q C 0.50
D C 0.44
I E 0.48
F E 0.66
I E 0.71
R E 0.67
F E 0.50
S C 0.48
K C 0.55
V C 0.64
D C 0.73
E C 0.51
D H 0.55
E H 0.69
A H 0.73
F H 0.76
V H 0.80
N H 0.77
T H 0.81
L H 0.86
N H 0.85
Y H 0.88
C H 0.91
K H 0.93
A H 0.93
L H 0.94
F H 0.94
A H 0.94
F H 0.94
I H 0.93
R H 0.90
K H 0.83
L H 0.73
H H 0.62
E H 0.56
D C 0.56
F C 0.54
K C 0.44
I E 0.65
E E 0.71
L E 0.69
H E 0.67
L E 0.55
D E 0.46
L C 0.51
N C 0.61
T C 0.51
K H 0.43
E H 0.48
Y H 0.46
V H 0.43
E C 0.42
D C 0.54
R C 0.63
T C 0.73
G C 0.80
T C 0.74
I C 0.67
P C 0.74
S C 0.72
V C 0.70
K C 0.79
P C 0.55
E C 0.48
K H 0.53
A H 0.63
S H 0.65
E H 0.69
F H 0.71
Y H 0.72
S H 0.71
V H 0.73
F H 0.66
K H 0.58
N C 0.48
I H 0.51
E H 0.49
D H 0.47
Q H 0.49
T C 0.49
D C 0.54
E C 0.49
R C 0.53
N C 0.59
S C 0.60
K C 0.50
K H 0.50
E H 0.49
Q C 0.45
L C 0.53
D C 0.66
D C 0.68
S C 0.70
S C 0.67
T C 0.62
Q C 0.52
Y E 0.45
K E 0.50
V C 0.47
D C 0.61
T C 0.59
N C 0.60
T C 0.54
L H 0.50
S C 0.50
D C 0.58
L C 0.77
P C 0.76
S H 0.56
D H 0.71
A H 0.79
L H 0.84
D H 0.85
Q H 0.84
L H 0.83
C H 0.79
K H 0.80
D H 0.78
I H 0.79
I H 0.72
E H 0.60
F H 0.51
R H 0.40
T C 0.39
K E 0.42
V E 0.60
V E 0.63
S E 0.59
I E 0.37
E C 0.40
K H 0.45
E H 0.50
K H 0.50
K H 0.52
M H 0.49
K H 0.49
S H 0.51
T H 0.53
Y H 0.59
E H 0.66
E H 0.69
S H 0.67
R H 0.70
R H 0.70
Q H 0.72
R H 0.78
H H 0.78
Q H 0.80
M H 0.84
Q H 0.85
K H 0.86
V H 0.86
F H 0.86
D H 0.85
Q H 0.82
I H 0.76
R H 0.66
K H 0.56
N C 0.55
H C 0.68
S C 0.71
G C 0.77
A C 0.74
K C 0.71
G C 0.74
S C 0.70
A C 0.61
N C 0.65
T C 0.60
E C 0.48
E C 0.46
E C 0.50
D C 0.57
T C 0.59
N C 0.66
M C 0.62
E C 0.61
D C 0.59
E C 0.51
D C 0.54
E C 0.48
E C 0.51
D C 0.61
D C 0.66
T C 0.56
E H 0.57
D H 0.58
D H 0.61
L H 0.68
A H 0.69
L H 0.71
E H 0.68
K H 0.66
R H 0.64
K H 0.65
E H 0.66
E H 0.66
R H 0.60
D H 0.56
L H 0.65
E H 0.67
E H 0.66
S H 0.56
N C 0.50
R H 0.50
R H 0.56
Y H 0.74
E H 0.83
D H 0.85
M H 0.87
L H 0.86
H H 0.82
Q H 0.77
L H 0.64
H C 0.49
S C 0.63
N C 0.75
T C 0.74
E C 0.74
P C 0.59
K C 0.48
I H 0.46
K H 0.50
S H 0.46
I H 0.48
R H 0.48
A H 0.58
D H 0.57
I H 0.56
M H 0.47
S C 0.50
A H 0.59
E H 0.63
N H 0.56
Y H 0.68
E H 0.78
E H 0.80
H H 0.76
L H 0.75
E H 0.73
K H 0.69
N H 0.49
R H 0.57
S H 0.66
L H 0.71
Y H 0.71
L H 0.83
K H 0.86
E H 0.86
L H 0.85
L H 0.79
H H 0.70
L H 0.64
A H 0.55
N C 0.50
D C 0.58
V C 0.54
H C 0.56
Y C 0.52
D C 0.55
H C 0.55
H C 0.54
R C 0.51
S C 0.48
F H 0.53
K H 0.59
E H 0.66
Q H 0.69
E H 0.66
E H 0.64
R H 0.59
R H 0.52
D H 0.49
E H 0.71
E H 0.72
D H 0.70
R H 0.69
A H 0.62
K H 0.51
N C 0.67
G C 0.79
N C 0.77
A C 0.56
K C 0.47
E C 0.44
L C 0.51
A C 0.60
P C 0.48
I E 0.53
Q E 0.59
L C 0.48
S C 0.66
D C 0.78
G C 0.79
K C 0.61
A E 0.53
I E 0.50
S C 0.45
A C 0.55
G C 0.65
K C 0.52
A E 0.45
A E 0.52
A E 0.62
I E 0.64
T E 0.62
L C 0.54
P C 0.71
E C 0.74
G C 0.73
T C 0.57
V E 0.51
K C 0.47
S C 0.54
E C 0.57
N C 0.62
Y C 0.63
N C 0.67
A C 0.64
D C 0.67
K C 0.65
N C 0.66
V C 0.58
S C 0.60
E C 0.57
S C 0.62
S C 0.59
E C 0.53
H C 0.45
V E 0.54
K E 0.67
I E 0.71
K E 0.67
F E 0.55
D E 0.42
F H 0.41
K H 0.52
K H 0.52
A H 0.51
I H 0.43
D C 0.47
H C 0.49
S C 0.52
V C 0.50
E C 0.54
S C 0.63
S C 0.68
S C 0.67
E C 0.64
D C 0.63
E C 0.64
G C 0.72
Y C 0.68
R C 0.62
E C 0.52
S C 0.58
E C 0.66
L C 0.78
P C 0.87
P C 0.84
T C 0.79
K C 0.83
P C 0.69
S C 0.62
E C 0.53
R C 0.49
S H 0.48
A H 0.56
A H 0.60
E H 0.58
D C 0.48
R C 0.58
L C 0.73
P C 0.75
F C 0.67
T C 0.70
A C 0.47
D H 0.47
E H 0.51
L C 0.40
N C 0.44
I E 0.50
R E 0.53
L E 0.46
T C 0.43
N C 0.54
L C 0.52
K C 0.50
E H 0.51
S H 0.54
R H 0.59
Y H 0.62
V H 0.80
D H 0.88
E H 0.91
L H 0.92
V H 0.93
R H 0.92
E H 0.90
F H 0.86
L H 0.74
G H 0.53
V H 0.49
Y C 0.48
E H 0.76
D H 0.86
E H 0.90
L H 0.92
V H 0.93
E H 0.92
Y H 0.90
I H 0.88
L H 0.86
E H 0.77
N H 0.56
I C 0.49
R C 0.50
V C 0.50
N C 0.59
Q H 0.57
S H 0.62
K H 0.75
Q H 0.84
A H 0.85
L H 0.85
L H 0.87
N H 0.85
E H 0.84
L H 0.80
R H 0.77
E H 0.74
T H 0.64
F H 0.43
D C 0.63
E C 0.61
D C 0.76
G C 0.77
E C 0.62
T C 0.42
I H 0.58
A H 0.64
D H 0.65
R H 0.66
L H 0.59
W H 0.54
S H 0.50
R H 0.55
K H 0.52
E H 0.47
F C 0.46
R C 0.52
L C 0.65
G C 0.84
T C 0.92
END