PFRMAT SS
TARGET YGL227W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGL227W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGL227W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGL227W.t2k.str2.rdb  (weight 1.54758)
METHOD YGL227W.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 YGL227W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGL227W
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 YGL227W.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 66
METHOD
METHOD ============================================
METHOD Comments from YGL227W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGL227W
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 YGL227W.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 66
METHOD
METHOD ============================================
METHOD Comments from YGL227W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGL227W
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 YGL227W.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 66
METHOD
METHOD ============================================
METHOD Comments from YGL227W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGL227W
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 YGL227W.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 66
METHOD
METHOD ============================================
MODEL 1
M C 0.84
S C 0.66
E H 0.48
Y H 0.53
M H 0.61
D H 0.64
D H 0.69
V H 0.68
D H 0.69
R H 0.94
E H 0.95
F H 0.95
I H 0.95
N H 0.92
C H 0.89
L H 0.81
F H 0.71
P H 0.81
S H 0.78
Y H 0.76
L H 0.69
L H 0.55
Q C 0.56
Q C 0.70
P C 0.69
V C 0.50
A E 0.52
Y E 0.70
D E 0.72
L E 0.72
W E 0.68
I E 0.66
L E 0.61
Y E 0.60
L E 0.48
Q C 0.41
H C 0.52
R C 0.42
K C 0.34
L H 0.38
F H 0.39
H H 0.43
K C 0.41
L C 0.51
K C 0.58
N C 0.74
T C 0.75
N C 0.73
L C 0.61
I C 0.54
N C 0.51
A C 0.51
D C 0.51
E C 0.55
N C 0.72
P C 0.73
T C 0.71
G C 0.77
V C 0.77
G C 0.74
M C 0.57
G C 0.51
R E 0.49
T E 0.47
K C 0.50
L C 0.58
T C 0.51
A H 0.62
L H 0.64
T H 0.62
R H 0.86
K H 0.90
E H 0.93
I H 0.94
W H 0.94
S H 0.94
K H 0.92
L H 0.91
M H 0.88
N H 0.75
L C 0.60
G C 0.89
V C 0.80
L C 0.54
G E 0.59
T E 0.80
I E 0.84
S E 0.81
F E 0.59
E E 0.49
A E 0.43
V C 0.47
N C 0.67
D H 0.57
D H 0.76
Y H 0.80
L H 0.75
I H 0.67
Q H 0.66
V H 0.67
Y H 0.61
K H 0.57
Y H 0.49
F C 0.50
Y C 0.72
P C 0.69
D C 0.74
V C 0.73
N C 0.81
D C 0.77
F C 0.70
T C 0.65
L C 0.65
R C 0.70
F C 0.71
G C 0.79
V C 0.72
K C 0.72
D C 0.73
S C 0.74
N C 0.78
K C 0.72
N C 0.68
S C 0.64
V C 0.52
R E 0.55
V E 0.47
M C 0.67
K C 0.59
A H 0.51
S H 0.59
S H 0.61
D H 0.58
M H 0.49
R C 0.59
K C 0.64
N C 0.57
A H 0.72
Q H 0.76
E H 0.79
L H 0.77
L H 0.72
E H 0.63
P H 0.62
V H 0.60
L H 0.58
S H 0.63
E H 0.71
R H 0.67
E H 0.64
M H 0.65
A H 0.59
L H 0.50
N C 0.58
S C 0.57
N C 0.53
T H 0.50
S C 0.48
L C 0.51
E C 0.50
N C 0.58
D C 0.66
R C 0.59
N C 0.57
D C 0.54
D C 0.53
D C 0.58
D C 0.55
D C 0.58
D C 0.63
D C 0.62
D C 0.66
D C 0.66
D C 0.57
D C 0.59
D C 0.55
D H 0.51
D C 0.50
D C 0.52
D C 0.54
D C 0.62
D C 0.67
D C 0.64
D C 0.61
D C 0.55
E H 0.69
S H 0.69
D H 0.67
L H 0.65
E H 0.56
S H 0.54
L H 0.51
E H 0.48
G C 0.58
E C 0.63
V C 0.58
D C 0.49
T H 0.50
D H 0.48
T C 0.47
D C 0.51
D C 0.57
N C 0.64
N C 0.70
E C 0.68
G C 0.63
D C 0.63
G C 0.63
S C 0.62
D C 0.67
N C 0.65
H C 0.70
E C 0.70
E C 0.70
G C 0.74
G C 0.79
E C 0.72
E C 0.58
G C 0.54
S C 0.51
R H 0.51
G H 0.52
A H 0.50
D C 0.53
A C 0.59
D C 0.67
V C 0.69
S C 0.70
S C 0.55
A C 0.54
Q C 0.53
Q C 0.52
R H 0.52
A H 0.65
E H 0.68
R H 0.67
V H 0.61
A H 0.51
D C 0.49
P C 0.48
W C 0.57
I C 0.64
Y C 0.71
Q C 0.65
R C 0.66
S C 0.63
R H 0.55
S H 0.59
A H 0.61
I H 0.54
N C 0.45
I C 0.45
E C 0.51
T C 0.51
E C 0.52
S H 0.54
R H 0.56
N H 0.49
L C 0.46
W C 0.49
D C 0.52
T C 0.58
S C 0.66
D C 0.69
K C 0.74
N C 0.79
S C 0.75
G C 0.70
L C 0.65
Q C 0.58
Y C 0.52
Y C 0.64
P C 0.75
P C 0.71
D C 0.73
Q C 0.72
S C 0.71
P C 0.66
S C 0.65
S C 0.64
S C 0.68
F C 0.64
S C 0.65
S C 0.67
P C 0.57
R C 0.47
V C 0.41
S C 0.42
S C 0.51
G C 0.65
N C 0.73
D C 0.73
K C 0.73
N C 0.71
D C 0.67
N C 0.64
E C 0.55
A C 0.52
T C 0.55
N C 0.62
V C 0.58
L C 0.56
S C 0.64
N C 0.73
S C 0.67
G C 0.67
S C 0.65
K C 0.65
K C 0.70
K C 0.75
N C 0.76
S C 0.73
M C 0.66
I C 0.66
P C 0.67
D C 0.59
I H 0.58
Y H 0.59
K H 0.61
I H 0.58
L H 0.52
G C 0.53
Y C 0.53
F C 0.51
L C 0.59
P C 0.62
S C 0.65
R C 0.62
W C 0.66
Q C 0.69
A C 0.65
Q C 0.65
P C 0.57
N C 0.51
N C 0.48
S H 0.49
L H 0.57
Q H 0.54
L C 0.46
S C 0.52
Q C 0.59
D C 0.64
G C 0.49
I E 0.61
T E 0.63
H E 0.48
L C 0.63
Q C 0.72
P C 0.74
N C 0.76
P C 0.74
D C 0.73
Y C 0.66
H C 0.64
S C 0.54
Y C 0.48
M C 0.52
T C 0.74
Y C 0.64
E C 0.70
R C 0.68
S C 0.66
S C 0.63
A C 0.59
S C 0.50
S E 0.51
A E 0.63
S E 0.64
T C 0.54
R C 0.76
N C 0.85
R C 0.74
L E 0.56
R E 0.80
T E 0.84
S E 0.82
F E 0.72
E C 0.55
N C 0.69
S C 0.65
G C 0.61
K C 0.55
V C 0.54
D C 0.59
F C 0.45
A E 0.55
V E 0.73
T E 0.78
W E 0.75
A E 0.53
N C 0.63
K C 0.64
S C 0.62
L C 0.70
P C 0.74
D C 0.79
N C 0.71
K C 0.57
L C 0.67
T C 0.71
I E 0.67
F E 0.87
Y E 0.91
Y E 0.92
E E 0.93
I E 0.92
K E 0.92
V E 0.88
L E 0.73
S E 0.53
V C 0.60
T C 0.65
S C 0.67
T C 0.62
E C 0.60
S C 0.61
A C 0.63
E C 0.65
N C 0.69
S C 0.71
N C 0.69
I C 0.55
V H 0.49
I H 0.75
G H 0.76
Y H 0.83
K H 0.86
L H 0.85
V H 0.85
E H 0.87
N H 0.85
E H 0.83
L H 0.77
M H 0.72
E H 0.62
A C 0.51
T C 0.70
T C 0.80
K C 0.83
K C 0.72
S C 0.68
V C 0.74
S C 0.81
R C 0.71
S C 0.62
S C 0.58
V C 0.54
A C 0.61
G C 0.65
S C 0.62
S C 0.54
S C 0.53
S C 0.55
L C 0.55
G C 0.67
G C 0.70
S C 0.64
N C 0.60
N C 0.62
M C 0.60
S C 0.59
S C 0.50
N C 0.51
R C 0.51
V C 0.56
P C 0.63
S C 0.65
T C 0.60
S C 0.50
F C 0.42
T C 0.39
M C 0.37
E C 0.41
G C 0.52
T C 0.63
Q C 0.69
R C 0.79
R C 0.72
D C 0.69
Y C 0.52
I E 0.77
Y E 0.89
E E 0.91
G E 0.88
G E 0.82
V E 0.75
S E 0.50
A C 0.59
M C 0.67
S C 0.66
L C 0.64
N C 0.69
V C 0.64
D C 0.70
G C 0.70
S C 0.61
I C 0.58
N C 0.65
K C 0.73
C C 0.68
Q C 0.61
K C 0.64
Y C 0.64
G C 0.66
F C 0.64
D C 0.69
L C 0.71
N C 0.73
V C 0.49
F E 0.67
G E 0.73
Y E 0.77
C E 0.53
G C 0.71
F C 0.84
D C 0.84
G C 0.64
L E 0.65
I E 0.72
T E 0.59
N C 0.58
S C 0.73
T C 0.77
E C 0.75
Q C 0.69
S C 0.66
K C 0.65
E C 0.61
Y C 0.69
A C 0.77
K C 0.76
P C 0.71
F C 0.70
G C 0.83
R C 0.85
D C 0.89
D C 0.69
V E 0.75
I E 0.86
G E 0.89
C E 0.90
G E 0.90
I E 0.87
N E 0.82
F C 0.59
I C 0.75
D C 0.83
G C 0.85
S E 0.78
I E 0.90
F E 0.90
F E 0.89
T E 0.78
K E 0.55
N C 0.89
G C 0.89
I C 0.59
H E 0.68
L E 0.57
G E 0.47
N E 0.42
A E 0.42
F E 0.42
T E 0.39
D C 0.55
L C 0.73
N C 0.83
D C 0.85
L C 0.78
E C 0.67
F E 0.51
V E 0.61
P E 0.67
Y E 0.80
V E 0.82
A E 0.80
L E 0.69
R C 0.67
P C 0.89
G C 0.92
N C 0.65
S E 0.79
I E 0.90
K E 0.92
T E 0.89
N E 0.77
F C 0.59
G C 0.79
L C 0.81
N C 0.82
E C 0.85
D C 0.78
F C 0.62
V C 0.50
F C 0.56
D C 0.74
I C 0.52
I H 0.53
G H 0.50
Y H 0.47
Q H 0.52
D H 0.63
K H 0.63
W H 0.51
K C 0.52
S C 0.51
L H 0.59
A H 0.60
Y H 0.60
E H 0.57
H H 0.57
I H 0.52
C H 0.44
R C 0.51
G C 0.70
R C 0.72
Q H 0.56
M H 0.62
D H 0.64
V H 0.60
S H 0.49
I C 0.55
E C 0.68
E C 0.67
F C 0.71
D C 0.80
S C 0.51
D H 0.61
E H 0.62
S H 0.57
E H 0.50
E C 0.52
D C 0.67
E C 0.67
T C 0.67
E C 0.73
N C 0.79
G C 0.80
P C 0.80
E C 0.81
E C 0.81
N C 0.83
K C 0.69
S C 0.53
T H 0.58
N H 0.69
V H 0.77
N H 0.78
E H 0.75
D H 0.74
L H 0.69
M H 0.63
D H 0.57
I H 0.50
D C 0.54
Q C 0.59
E C 0.52
D C 0.56
G C 0.54
A C 0.55
A C 0.61
G C 0.65
N C 0.59
K C 0.54
D H 0.50
T H 0.63
K H 0.61
K H 0.65
L H 0.63
N H 0.56
D H 0.58
E H 0.61
K H 0.54
D C 0.53
N C 0.64
N C 0.70
L C 0.68
K C 0.54
F E 0.47
L E 0.51
L E 0.49
G C 0.57
E C 0.64
D C 0.58
N C 0.52
R E 0.40
F E 0.47
I E 0.43
D C 0.37
G C 0.44
K C 0.41
L C 0.39
V C 0.46
R C 0.54
P C 0.56
D C 0.60
V C 0.59
N C 0.70
N C 0.77
I C 0.65
N C 0.67
N C 0.63
L C 0.49
S C 0.48
V H 0.56
D H 0.58
D H 0.67
G H 0.64
S H 0.57
L H 0.71
P H 0.89
N H 0.90
T H 0.92
L H 0.93
N H 0.94
V H 0.94
M H 0.95
I H 0.94
N H 0.94
D H 0.94
Y H 0.93
L H 0.90
I H 0.86
H H 0.77
E H 0.59
G C 0.64
L H 0.72
V H 0.93
D H 0.95
V H 0.95
A H 0.95
K H 0.95
G H 0.94
F H 0.93
L H 0.92
K H 0.90
D H 0.85
L H 0.70
Q H 0.49
K C 0.52
D C 0.67
A C 0.71
V C 0.68
N C 0.71
V C 0.73
N C 0.78
G C 0.79
Q C 0.80
H C 0.77
S C 0.59
E C 0.56
S C 0.50
K H 0.58
D H 0.60
V H 0.58
I H 0.52
R H 0.46
H C 0.49
N C 0.63
E C 0.68
R C 0.64
Q C 0.68
I C 0.66
M C 0.58
K C 0.55
E C 0.48
E H 0.83
R H 0.84
M H 0.88
V H 0.92
K H 0.93
I H 0.94
R H 0.95
Q H 0.96
E H 0.96
L H 0.96
R H 0.96
Y H 0.96
L H 0.96
I H 0.94
N H 0.90
K H 0.60
G C 0.65
Q C 0.64
I H 0.82
S H 0.93
K H 0.95
C H 0.95
I H 0.96
N H 0.95
Y H 0.94
I H 0.92
D H 0.88
N H 0.78
E H 0.65
I C 0.56
P H 0.74
D H 0.80
L H 0.80
L H 0.75
K H 0.62
N C 0.51
N C 0.79
L C 0.50
E H 0.51
L H 0.65
V H 0.63
F H 0.60
E H 0.63
L H 0.65
K H 0.69
L H 0.75
A H 0.79
N H 0.72
Y H 0.79
L H 0.82
V H 0.79
M H 0.77
I H 0.61
K H 0.46
K C 0.62
S C 0.81
S C 0.80
S H 0.67
K H 0.84
D H 0.88
D H 0.91
D H 0.91
E H 0.91
I H 0.89
E H 0.80
N H 0.70
L H 0.66
I H 0.67
L H 0.62
K H 0.47
G C 0.68
Q C 0.75
E C 0.69
L C 0.71
S C 0.75
N C 0.70
E C 0.70
F C 0.56
I E 0.47
Y E 0.54
D E 0.57
T E 0.67
K E 0.68
I E 0.57
P C 0.52
Q C 0.70
S C 0.64
L C 0.68
R H 0.52
D H 0.80
R H 0.80
F H 0.87
S H 0.92
G H 0.92
Q H 0.91
L H 0.90
S H 0.82
N H 0.58
V H 0.68
S H 0.69
A H 0.70
L H 0.58
L C 0.53
A C 0.69
Y C 0.72
S C 0.76
N C 0.83
P C 0.81
L C 0.78
V C 0.55
E C 0.56
A H 0.52
P C 0.50
K C 0.51
E C 0.56
I C 0.52
S C 0.45
G E 0.58
Y E 0.64
L E 0.49
S C 0.63
D C 0.72
E C 0.62
Y C 0.52
L H 0.35
Q E 0.47
E E 0.48
R E 0.43
L C 0.41
F C 0.56
Q C 0.70
V C 0.73
S C 0.78
N C 0.77
N C 0.70
T C 0.65
I C 0.68
L C 0.59
T C 0.53
F C 0.54
L C 0.59
H C 0.69
K C 0.78
D C 0.72
S C 0.50
E C 0.47
C C 0.53
A C 0.52
L C 0.47
E E 0.44
N E 0.52
V E 0.54
I C 0.60
S C 0.76
N C 0.80
T C 0.63
R E 0.74
A E 0.90
M E 0.92
L E 0.91
S E 0.90
T E 0.85
L E 0.67
L C 0.48
E C 0.75
Y C 0.79
N C 0.60
A E 0.55
F E 0.50
G C 0.58
S C 0.68
T C 0.74
N C 0.81
S C 0.82
S C 0.79
D C 0.82
P C 0.78
R C 0.64
Y E 0.48
Y E 0.51
K E 0.47
A E 0.50
I E 0.47
N C 0.47
F C 0.57
D C 0.75
E C 0.71
D C 0.70
V C 0.68
L C 0.65
N C 0.69
L C 0.91
END