PFRMAT SS
TARGET YBR233W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YBR233W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YBR233W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YBR233W.t2k.str2.rdb  (weight 1.54758)
METHOD YBR233W.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 YBR233W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YBR233W
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 YBR233W.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 169
METHOD
METHOD ============================================
METHOD Comments from YBR233W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YBR233W
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 YBR233W.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 169
METHOD
METHOD ============================================
METHOD Comments from YBR233W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YBR233W
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 YBR233W.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 169
METHOD
METHOD ============================================
METHOD Comments from YBR233W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YBR233W
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 YBR233W.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 169
METHOD
METHOD ============================================
MODEL 1
M C 0.84
S C 0.73
T C 0.69
E C 0.58
T H 0.41
T H 0.48
K H 0.53
P H 0.59
S H 0.62
I H 0.60
T H 0.55
T H 0.50
T C 0.61
P C 0.81
T C 0.65
T E 0.60
V E 0.78
L E 0.78
V E 0.70
S C 0.56
P C 0.75
N C 0.76
T C 0.75
L C 0.76
K C 0.71
R C 0.72
K C 0.73
K C 0.70
G C 0.54
E E 0.52
D E 0.50
T C 0.56
S C 0.75
E C 0.81
E C 0.65
Q H 0.49
L H 0.58
E H 0.65
A H 0.80
E H 0.86
I H 0.89
K H 0.90
R H 0.90
V H 0.88
A H 0.85
L H 0.82
K H 0.82
D H 0.82
A H 0.78
D H 0.72
S H 0.63
H C 0.48
S C 0.69
D C 0.79
N C 0.81
D C 0.78
H C 0.76
D C 0.73
S C 0.69
P C 0.71
D C 0.75
N C 0.80
V C 0.78
P C 0.78
S C 0.73
D C 0.56
V E 0.68
H E 0.78
L E 0.85
R E 0.89
M E 0.88
L E 0.87
C E 0.79
L E 0.50
V C 0.44
K H 0.47
H H 0.41
A C 0.38
S E 0.49
L E 0.69
I E 0.71
V E 0.67
G C 0.74
H C 0.86
K C 0.87
G C 0.52
A H 0.71
T H 0.83
I H 0.93
S H 0.94
R H 0.94
I H 0.95
K H 0.94
S H 0.92
E H 0.83
T C 0.57
S C 0.92
A C 0.80
R E 0.62
I E 0.80
N E 0.77
I E 0.57
S C 0.71
N C 0.82
N C 0.83
I C 0.83
R C 0.81
G C 0.83
V C 0.82
P C 0.75
E C 0.63
R E 0.51
I E 0.80
V E 0.88
Y E 0.91
V E 0.87
R E 0.64
G C 0.79
T C 0.89
C C 0.48
D H 0.61
D H 0.66
V H 0.87
A H 0.93
K H 0.94
A H 0.95
Y H 0.96
G H 0.96
M H 0.95
I H 0.95
V H 0.96
R H 0.95
A H 0.95
L H 0.94
L H 0.91
E H 0.83
E H 0.73
H H 0.54
G C 0.60
N C 0.71
E C 0.74
D C 0.75
N C 0.74
G C 0.76
E C 0.79
D C 0.80
I C 0.78
E C 0.66
I E 0.70
S E 0.84
I E 0.89
N E 0.91
L E 0.90
L E 0.88
I E 0.73
P C 0.63
H H 0.57
H H 0.60
L H 0.57
M C 0.54
G C 0.48
C E 0.65
I E 0.69
I E 0.66
G C 0.76
K C 0.87
R C 0.89
G C 0.67
S H 0.54
R H 0.71
L H 0.92
R H 0.93
E H 0.93
I H 0.94
E H 0.93
D H 0.90
L H 0.78
S C 0.60
A C 0.92
A C 0.77
K E 0.64
L E 0.86
F E 0.85
A E 0.72
S C 0.62
P C 0.80
N C 0.79
Q C 0.75
L C 0.75
L C 0.74
L C 0.78
S C 0.78
N C 0.77
D C 0.67
R E 0.51
I E 0.80
L E 0.87
T E 0.90
I E 0.86
N E 0.56
G C 0.85
V C 0.90
P H 0.84
D H 0.92
A H 0.93
I H 0.95
H H 0.96
I H 0.96
A H 0.96
T H 0.96
F H 0.96
Y H 0.96
I H 0.96
S H 0.96
Q H 0.95
T H 0.94
L H 0.92
L H 0.86
N H 0.69
F C 0.59
Q C 0.71
M C 0.70
E C 0.74
S C 0.71
P C 0.58
Q C 0.49
K C 0.49
N C 0.53
V C 0.54
K C 0.54
R C 0.54
S C 0.59
I C 0.60
Y C 0.61
Y C 0.67
Q C 0.73
P C 0.66
T C 0.60
Q C 0.58
F C 0.60
N C 0.62
S C 0.60
V C 0.60
L C 0.65
I C 0.75
D C 0.73
H C 0.72
S C 0.70
Q C 0.62
P C 0.52
N C 0.49
T C 0.49
I C 0.48
F C 0.53
H C 0.61
Q C 0.61
R C 0.60
N C 0.60
H C 0.60
Q C 0.60
Y C 0.63
H C 0.66
P C 0.68
S C 0.69
D C 0.69
K C 0.67
L C 0.66
L C 0.70
S C 0.74
Y C 0.70
K C 0.71
P C 0.66
N C 0.63
K C 0.59
N C 0.60
L C 0.67
P C 0.70
I C 0.64
S C 0.63
S C 0.63
T C 0.63
L C 0.64
L C 0.69
S C 0.69
M C 0.65
A C 0.63
T C 0.61
P C 0.62
Q C 0.66
Y C 0.72
T C 0.71
T C 0.72
A C 0.74
S C 0.71
V C 0.67
A C 0.65
N C 0.65
A C 0.58
T C 0.53
A C 0.53
F C 0.57
Q C 0.65
P C 0.71
N C 0.71
F C 0.66
V C 0.63
I C 0.62
P C 0.59
N C 0.58
V C 0.55
T C 0.55
V C 0.55
L C 0.57
D C 0.58
G C 0.56
P C 0.54
V C 0.54
I C 0.57
S C 0.62
P C 0.66
A C 0.70
P C 0.69
G C 0.69
N C 0.70
H C 0.71
L C 0.68
L C 0.70
M C 0.70
N C 0.64
F E 0.57
V E 0.80
Q E 0.87
Q E 0.89
E E 0.91
I E 0.89
F E 0.87
I E 0.71
D C 0.65
E H 0.59
K H 0.62
F H 0.62
V C 0.50
G C 0.57
N E 0.51
V E 0.63
I E 0.59
G C 0.72
K C 0.84
D C 0.88
G C 0.70
K H 0.45
H H 0.60
I H 0.92
N H 0.94
S H 0.94
V H 0.93
K H 0.93
E H 0.91
S H 0.80
T C 0.61
G C 0.92
C C 0.83
S E 0.58
I E 0.83
I E 0.84
I E 0.68
Q C 0.66
D C 0.83
P C 0.81
V C 0.80
E C 0.77
G C 0.82
S C 0.80
S C 0.80
E C 0.77
R C 0.64
R E 0.79
L E 0.88
T E 0.91
I E 0.86
R E 0.59
G C 0.84
T C 0.92
F H 0.86
M H 0.93
A H 0.94
S H 0.96
Q H 0.96
A H 0.96
A H 0.96
I H 0.96
M H 0.96
L H 0.96
I H 0.96
S H 0.95
N H 0.94
K H 0.93
I H 0.91
E H 0.85
I H 0.72
D H 0.64
R H 0.63
S H 0.57
N C 0.49
A C 0.55
E C 0.58
R C 0.54
K E 0.51
R E 0.69
R E 0.75
S E 0.64
P C 0.66
L C 0.91
END