PFRMAT SS
TARGET YGR229C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR229C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR229C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR229C.t2k.str2.rdb  (weight 1.54758)
METHOD YGR229C.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 YGR229C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR229C
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 YGR229C.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 9
METHOD
METHOD ============================================
METHOD Comments from YGR229C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR229C
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 YGR229C.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 9
METHOD
METHOD ============================================
METHOD Comments from YGR229C.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR229C
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 YGR229C.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 9
METHOD
METHOD ============================================
METHOD Comments from YGR229C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR229C
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 YGR229C.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 9
METHOD
METHOD ============================================
MODEL 1
M C 0.84
D C 0.53
L H 0.61
F H 0.65
K H 0.71
R H 0.69
K H 0.62
V H 0.61
K H 0.59
E H 0.57
W H 0.57
V H 0.43
Y E 0.46
S E 0.46
L C 0.47
S C 0.67
T C 0.75
D C 0.79
D C 0.69
H C 0.58
Y C 0.47
A C 0.47
E C 0.53
Y C 0.61
N C 0.83
P C 0.78
D C 0.81
E C 0.79
T C 0.84
P C 0.75
T C 0.64
F C 0.57
N C 0.61
M C 0.66
G C 0.71
K C 0.56
R C 0.53
L C 0.48
N C 0.52
S C 0.60
N C 0.70
N C 0.74
G C 0.76
Q C 0.70
V C 0.66
N C 0.76
P C 0.50
S C 0.51
Q H 0.45
M C 0.52
H C 0.51
L C 0.50
N C 0.64
S C 0.76
V C 0.79
D C 0.81
E C 0.80
E C 0.74
M C 0.66
S C 0.67
M C 0.60
G C 0.60
F C 0.57
Q C 0.66
N C 0.82
G C 0.88
V C 0.86
P C 0.78
S C 0.81
N C 0.80
E C 0.75
D C 0.71
I C 0.64
N C 0.66
I C 0.49
D C 0.47
E C 0.45
F C 0.51
T C 0.77
S C 0.83
T C 0.88
E C 0.88
S C 0.89
N C 0.83
D C 0.82
G C 0.65
V H 0.57
S H 0.68
E H 0.76
T H 0.87
L H 0.90
L H 0.90
A H 0.91
W H 0.93
R H 0.92
H H 0.91
I H 0.92
D H 0.93
F H 0.93
W H 0.93
T H 0.90
S H 0.88
E H 0.74
H H 0.53
N C 0.77
P H 0.57
D H 0.60
L H 0.70
N H 0.65
A H 0.61
T H 0.49
L C 0.59
S C 0.73
D C 0.80
P C 0.87
C C 0.82
T C 0.86
Q H 0.89
N H 0.90
D H 0.93
I H 0.95
T H 0.95
H H 0.94
A H 0.95
E H 0.94
E H 0.92
D H 0.87
L H 0.60
E C 0.74
V C 0.73
S C 0.73
F C 0.82
P C 0.86
N H 0.63
P H 0.72
V H 0.74
K H 0.78
A H 0.77
S H 0.73
F H 0.61
K H 0.52
I H 0.51
H C 0.55
D C 0.76
G C 0.81
Q C 0.59
E C 0.45
D C 0.48
L C 0.60
E C 0.71
S C 0.74
M C 0.74
T C 0.77
G C 0.81
T C 0.70
S C 0.64
G C 0.58
L C 0.53
F C 0.50
Y C 0.60
G C 0.69
F C 0.58
Q C 0.46
L E 0.51
M C 0.58
T C 0.79
L H 0.93
D H 0.93
Q H 0.94
V H 0.94
V H 0.93
A H 0.87
M H 0.86
T H 0.85
Q H 0.87
A H 0.87
W H 0.88
R H 0.89
N H 0.86
V H 0.84
A H 0.79
K H 0.75
N H 0.66
L H 0.48
N C 0.67
K H 0.70
R H 0.70
S H 0.67
Q H 0.65
Q H 0.60
G C 0.50
L H 0.55
S H 0.61
H H 0.65
V H 0.63
T H 0.59
S H 0.56
T H 0.52
G C 0.56
S C 0.52
S C 0.46
S C 0.46
S C 0.52
M C 0.48
E C 0.52
R C 0.60
L C 0.67
N C 0.72
G C 0.66
N C 0.64
K C 0.55
F C 0.50
K C 0.55
L C 0.47
P C 0.48
N C 0.53
I C 0.66
P C 0.57
D C 0.49
Q C 0.48
K C 0.53
S C 0.63
I C 0.80
P C 0.87
P H 0.67
N H 0.64
A H 0.70
V H 0.58
Q H 0.54
P H 0.56
V H 0.53
Y C 0.41
A C 0.56
H C 0.82
P C 0.72
A C 0.71
W C 0.53
I C 0.54
P C 0.51
L C 0.52
I C 0.58
T C 0.68
D C 0.80
N C 0.78
A C 0.81
G C 0.80
N C 0.74
H E 0.52
I E 0.80
G E 0.87
V E 0.87
D E 0.81
L E 0.65
A C 0.50
P C 0.64
G C 0.84
P C 0.87
N C 0.90
G C 0.87
K C 0.72
Y E 0.60
A E 0.70
Q E 0.87
I E 0.90
I E 0.89
T E 0.86
F E 0.67
G C 0.55
R C 0.66
D C 0.68
F C 0.75
D C 0.80
T C 0.76
K C 0.54
F E 0.41
V E 0.55
I E 0.57
A E 0.45
E H 0.36
N C 0.45
W H 0.89
G H 0.94
E H 0.95
F H 0.95
L H 0.96
L H 0.96
S H 0.95
F H 0.95
A H 0.93
N H 0.85
D H 0.62
L H 0.52
E C 0.50
A C 0.71
G C 0.87
N C 0.75
W E 0.64
Y E 0.70
L E 0.75
V E 0.54
D C 0.67
D C 0.82
N C 0.78
D C 0.73
D C 0.64
Y C 0.60
F C 0.65
S C 0.71
G C 0.77
D C 0.78
G C 0.50
E H 0.51
L H 0.48
V H 0.38
F E 0.46
R E 0.48
D E 0.41
K C 0.61
K C 0.80
S C 0.83
N C 0.84
G C 0.85
P C 0.75
I C 0.65
Q C 0.49
D H 0.54
Y H 0.81
F H 0.91
E H 0.92
V H 0.92
L H 0.89
K H 0.83
R H 0.77
R H 0.67
T H 0.52
W H 0.50
I H 0.75
K H 0.76
Y H 0.73
Q H 0.70
E H 0.70
N H 0.70
L H 0.71
R H 0.71
S H 0.71
Q H 0.67
Q H 0.59
Q H 0.47
K C 0.58
S C 0.67
Q C 0.74
P C 0.74
D C 0.71
T C 0.65
S C 0.63
L C 0.60
Q C 0.63
E C 0.65
Q C 0.77
K C 0.83
Y C 0.79
V C 0.78
P C 0.84
A C 0.84
S C 0.82
Q C 0.49
K C 0.50
K C 0.47
V C 0.60
A C 0.64
A C 0.65
E C 0.71
Q C 0.79
P C 0.78
S C 0.74
T C 0.76
L C 0.73
N C 0.58
A E 0.54
E E 0.64
S E 0.57
I C 0.54
K C 0.70
G C 0.79
E C 0.71
D C 0.76
S C 0.78
G C 0.83
S C 0.78
A C 0.76
D C 0.67
V C 0.56
Q C 0.58
S C 0.53
V C 0.59
Q C 0.71
D C 0.83
H C 0.83
E C 0.83
S C 0.80
V H 0.70
K H 0.75
I H 0.78
V H 0.63
K H 0.46
T C 0.50
E C 0.64
P H 0.49
S H 0.51
E C 0.50
A C 0.71
E C 0.81
T C 0.77
T C 0.63
T C 0.51
V C 0.47
N C 0.53
T C 0.57
E C 0.47
S C 0.49
L C 0.59
G C 0.73
Q C 0.72
A C 0.54
E C 0.54
H C 0.61
E C 0.70
I C 0.68
K C 0.72
A C 0.59
D C 0.59
N C 0.67
V C 0.63
D C 0.56
I C 0.52
K C 0.76
Q C 0.75
E C 0.80
S C 0.83
E C 0.49
R H 0.50
K H 0.52
E H 0.60
D H 0.53
E H 0.53
K C 0.49
Q C 0.63
P C 0.66
K C 0.55
V C 0.57
E C 0.60
E C 0.68
K H 0.51
E H 0.56
H H 0.55
V H 0.49
E C 0.48
N C 0.66
E C 0.76
H C 0.72
V C 0.62
T C 0.64
E C 0.52
S C 0.56
A C 0.51
K C 0.65
K C 0.64
D C 0.72
D C 0.66
D C 0.57
V H 0.54
N H 0.59
K H 0.68
Q H 0.66
T H 0.62
E H 0.72
E H 0.74
M H 0.69
N H 0.66
K H 0.75
K H 0.76
E H 0.77
E H 0.80
N H 0.75
E H 0.69
I H 0.54
R H 0.45
S C 0.56
D C 0.62
D C 0.62
A C 0.50
K C 0.48
V H 0.62
E H 0.72
E H 0.69
A H 0.72
R H 0.77
E H 0.73
E H 0.71
F H 0.58
E H 0.55
N C 0.56
I C 0.67
A C 0.78
L C 0.91
END