PFRMAT SS
TARGET YGR017W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR017W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR017W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR017W.t2k.str2.rdb  (weight 1.54758)
METHOD YGR017W.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 YGR017W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR017W
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 YGR017W.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 8
METHOD
METHOD ============================================
METHOD Comments from YGR017W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR017W
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 YGR017W.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 8
METHOD
METHOD ============================================
METHOD Comments from YGR017W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR017W
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 YGR017W.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 8
METHOD
METHOD ============================================
METHOD Comments from YGR017W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR017W
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 YGR017W.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 8
METHOD
METHOD ============================================
MODEL 1
M C 0.85
S C 0.72
H C 0.68
Q C 0.68
M C 0.70
A C 0.51
P H 0.70
W H 0.81
I H 0.90
P H 0.94
M H 0.95
F H 0.95
I H 0.95
Q H 0.94
S H 0.90
C H 0.81
K H 0.62
N C 0.64
N C 0.84
T C 0.87
E C 0.86
P C 0.81
F C 0.72
V C 0.52
S E 0.64
F E 0.74
Q E 0.81
F E 0.82
A E 0.80
T E 0.77
V E 0.68
D E 0.53
E C 0.69
L C 0.77
T C 0.87
N C 0.91
K C 0.84
P C 0.59
R C 0.50
C E 0.55
R E 0.65
T E 0.82
V E 0.88
V E 0.87
F E 0.81
R E 0.64
D E 0.42
F E 0.37
L E 0.34
F C 0.48
H C 0.68
D C 0.71
K C 0.72
R C 0.72
T C 0.81
N C 0.83
V E 0.68
L E 0.87
T E 0.88
F E 0.86
N E 0.68
T C 0.54
D C 0.73
M C 0.64
R C 0.65
S C 0.48
S H 0.55
K H 0.59
I H 0.59
T H 0.59
E H 0.51
S C 0.42
F C 0.55
I C 0.62
T C 0.81
P C 0.83
N C 0.86
S C 0.82
N C 0.79
N C 0.71
S C 0.73
S C 0.72
D C 0.73
S C 0.75
K C 0.74
R C 0.74
C C 0.74
E C 0.80
T C 0.77
P C 0.59
F C 0.43
F E 0.42
E E 0.51
A E 0.59
C E 0.69
F E 0.69
Y E 0.66
F C 0.59
P C 0.80
E C 0.83
T C 0.72
W C 0.46
E E 0.46
Q E 0.66
Y E 0.79
R E 0.82
F E 0.76
S C 0.55
G C 0.65
Q E 0.66
C E 0.81
F E 0.80
T E 0.74
I C 0.46
S C 0.66
K H 0.55
Q H 0.54
F H 0.62
K H 0.50
K C 0.57
I C 0.70
P C 0.74
A C 0.45
E H 0.52
I H 0.45
V C 0.54
T C 0.61
K C 0.55
Y C 0.56
D C 0.62
I C 0.61
F C 0.65
S C 0.76
P C 0.61
R C 0.56
F C 0.51
S C 0.59
E C 0.63
T C 0.72
N C 0.79
D C 0.77
D C 0.79
S C 0.68
T C 0.64
D C 0.57
E C 0.50
E C 0.51
I C 0.61
D C 0.70
T C 0.77
P C 0.78
I C 0.73
N C 0.79
D C 0.79
D C 0.79
D C 0.80
D C 0.80
D C 0.79
D C 0.78
K C 0.77
N C 0.79
N C 0.79
D C 0.73
A C 0.72
D C 0.74
N C 0.80
N C 0.72
D C 0.65
I C 0.61
N C 0.69
E C 0.59
D C 0.59
N H 0.51
K H 0.60
L H 0.65
I H 0.67
E H 0.66
S H 0.58
I H 0.55
E C 0.51
N C 0.66
D C 0.74
E C 0.68
H C 0.70
H C 0.77
E C 0.68
D C 0.82
E C 0.83
D C 0.87
D C 0.87
Y C 0.79
Y C 0.69
P C 0.78
Q C 0.79
P C 0.70
Q C 0.57
E H 0.48
W H 0.62
E H 0.79
A H 0.88
E H 0.90
L H 0.91
L H 0.91
R H 0.91
Q H 0.89
W H 0.87
S H 0.85
S H 0.73
L H 0.55
S C 0.67
R H 0.78
H H 0.76
T H 0.73
K H 0.67
S H 0.54
L H 0.45
Y C 0.52
R C 0.65
K C 0.76
P C 0.81
A C 0.85
P C 0.86
G C 0.89
Q C 0.80
K C 0.68
L C 0.66
T C 0.68
S C 0.56
E H 0.46
T H 0.55
S H 0.55
K H 0.59
Q H 0.55
L C 0.52
D C 0.57
K C 0.62
L C 0.64
H C 0.75
R C 0.68
G C 0.73
V C 0.71
D C 0.75
G C 0.73
A C 0.62
K C 0.56
E C 0.51
D C 0.57
A C 0.70
G C 0.79
L C 0.77
E C 0.77
N C 0.78
F E 0.49
G E 0.81
I E 0.92
V E 0.92
C E 0.92
L E 0.87
C E 0.69
V C 0.48
D C 0.60
S C 0.44
V E 0.50
D E 0.43
F E 0.54
L E 0.51
N E 0.61
L C 0.54
K C 0.65
E C 0.75
G C 0.86
R C 0.83
G C 0.84
G C 0.72
E E 0.60
R E 0.79
W E 0.84
I E 0.80
F E 0.70
Q E 0.53
K C 0.54
T C 0.67
D C 0.83
G C 0.84
K C 0.79
D C 0.75
E C 0.56
D C 0.48
L C 0.39
W C 0.41
E E 0.41
E E 0.53
Q E 0.56
E E 0.56
V C 0.62
C C 0.86
P C 0.92
END