PFRMAT SS
TARGET YDR018C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YDR018C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YDR018C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YDR018C.t2k.str.rdb  (weight 1.53983)
METHOD YDR018C.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 YDR018C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YDR018C
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 YDR018C.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 57
METHOD
METHOD ============================================
METHOD Comments from YDR018C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YDR018C
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 YDR018C.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 57
METHOD
METHOD ============================================
METHOD Comments from YDR018C.t2k.str.rdb
METHOD ============================================
METHOD TARGET YDR018C
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.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 str )
METHOD The input amino acid frequencies were determined from
METHOD alignment YDR018C.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 57
METHOD
METHOD ============================================
METHOD Comments from YDR018C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YDR018C
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 YDR018C.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 57
METHOD
METHOD ============================================
MODEL 1
M C 0.89
K C 0.76
H C 0.67
S C 0.60
Q C 0.54
K H 0.54
Y H 0.61
R H 0.67
R H 0.66
Y H 0.63
G H 0.56
I H 0.61
Y H 0.65
E H 0.66
K H 0.71
T H 0.82
G H 0.86
N H 0.89
P H 0.93
F H 0.94
I H 0.95
K H 0.95
G H 0.95
L H 0.95
Q H 0.95
R H 0.96
L H 0.96
L H 0.96
I H 0.96
A H 0.96
C H 0.96
L H 0.96
F H 0.95
I H 0.95
S H 0.94
G H 0.94
S H 0.95
L H 0.96
S H 0.96
I H 0.96
V H 0.95
V H 0.94
F H 0.91
Q H 0.88
I H 0.83
C H 0.78
L H 0.69
Q H 0.58
V H 0.46
L H 0.49
L H 0.48
P H 0.48
W H 0.48
S H 0.57
K H 0.82
I H 0.84
R H 0.86
F H 0.90
Q H 0.91
N H 0.93
G H 0.93
I H 0.94
N H 0.94
Q H 0.94
S H 0.95
K H 0.95
K H 0.96
A H 0.95
F H 0.95
I H 0.95
V H 0.95
L H 0.95
L H 0.95
C H 0.96
M H 0.96
I H 0.95
L H 0.95
N H 0.93
M H 0.87
V H 0.73
A C 0.61
P C 0.91
S C 0.82
S E 0.53
L E 0.80
N E 0.87
V E 0.88
T E 0.75
F C 0.56
E C 0.80
T C 0.78
S C 0.67
R C 0.65
P C 0.59
L C 0.61
K C 0.67
N C 0.75
S C 0.74
S C 0.64
N C 0.60
A C 0.56
K C 0.56
P C 0.57
C C 0.62
F C 0.71
R C 0.70
F C 0.72
K C 0.77
D C 0.76
R C 0.68
A E 0.77
I E 0.92
I E 0.92
I E 0.89
A E 0.73
N C 0.64
H C 0.77
Q C 0.73
M C 0.66
Y H 0.66
A H 0.71
D H 0.81
W H 0.93
I H 0.95
Y H 0.95
L H 0.95
W H 0.94
W H 0.93
L H 0.87
S H 0.77
F H 0.64
V H 0.56
S C 0.69
N C 0.89
L C 0.84
G C 0.75
G C 0.66
N C 0.53
V C 0.34
Y E 0.56
I E 0.60
I E 0.58
L E 0.44
K H 0.58
K H 0.67
A H 0.66
L H 0.56
Q H 0.46
Y C 0.51
I C 0.65
P C 0.59
L H 0.67
L H 0.78
G H 0.82
F H 0.89
G H 0.89
M H 0.87
R H 0.82
N H 0.73
F H 0.52
K C 0.69
F C 0.63
I C 0.46
F E 0.40
L E 0.40
S C 0.45
R C 0.60
N C 0.71
W C 0.57
Q C 0.53
K C 0.58
D C 0.70
E H 0.92
K H 0.94
A H 0.94
L H 0.94
T H 0.93
N H 0.90
S H 0.86
L H 0.86
V H 0.85
S H 0.81
M H 0.70
D H 0.61
L H 0.62
N H 0.56
A H 0.63
R H 0.69
C H 0.62
K H 0.48
G H 0.52
P H 0.72
L H 0.73
T H 0.70
N H 0.60
Y H 0.50
K C 0.62
S C 0.66
C C 0.65
Y C 0.58
S C 0.58
K C 0.60
T C 0.63
N C 0.69
E C 0.72
S C 0.76
I C 0.80
A C 0.83
A C 0.79
Y E 0.62
N E 0.86
L E 0.91
I E 0.91
M E 0.86
F E 0.58
P C 0.68
E C 0.80
G C 0.80
T C 0.78
N C 0.77
L C 0.76
S C 0.75
L H 0.88
K H 0.90
T H 0.91
R H 0.91
E H 0.92
K H 0.91
S H 0.90
E H 0.94
A H 0.95
F H 0.96
C H 0.95
Q H 0.95
R H 0.91
A C 0.56
H C 0.94
L C 0.93
D C 0.85
H C 0.72
V C 0.78
Q C 0.75
L C 0.59
R C 0.55
H C 0.59
L C 0.62
L C 0.53
L C 0.65
P C 0.68
H C 0.68
S C 0.50
K H 0.60
G H 0.88
L H 0.95
K H 0.96
F H 0.96
A H 0.95
V H 0.95
E H 0.94
K H 0.88
L H 0.76
A H 0.80
P H 0.69
S H 0.60
L C 0.56
D C 0.58
A E 0.42
I E 0.68
Y E 0.81
D E 0.77
V E 0.76
T E 0.76
I E 0.74
G E 0.62
Y C 0.67
S C 0.81
P C 0.88
A C 0.86
L C 0.83
R C 0.69
T C 0.60
E C 0.60
Y C 0.54
V C 0.57
G C 0.69
T C 0.71
K C 0.78
F C 0.73
T C 0.68
L H 0.77
K H 0.84
K H 0.82
I H 0.79
F H 0.70
L H 0.51
M C 0.71
G C 0.85
V C 0.77
Y C 0.76
P C 0.77
E C 0.72
K E 0.60
V E 0.79
D E 0.87
F E 0.92
Y E 0.92
I E 0.90
R E 0.86
E E 0.80
F E 0.62
R C 0.60
V C 0.70
N C 0.72
E C 0.65
I C 0.82
P C 0.81
L C 0.71
Q C 0.66
D C 0.68
D H 0.73
E H 0.85
V H 0.87
F H 0.94
F H 0.95
N H 0.95
W H 0.95
L H 0.95
L H 0.94
G H 0.92
V H 0.92
W H 0.90
K H 0.90
E H 0.87
K H 0.92
D H 0.94
Q H 0.95
L H 0.95
L H 0.95
E H 0.95
D H 0.94
Y H 0.93
Y H 0.88
N H 0.82
T H 0.50
G C 0.87
Q C 0.86
F C 0.80
K C 0.84
S C 0.83
N C 0.80
A C 0.76
K C 0.71
N C 0.72
D C 0.70
N C 0.59
Q C 0.53
S C 0.53
I C 0.52
V C 0.53
V C 0.49
T C 0.49
T C 0.57
Q C 0.65
T C 0.68
T C 0.50
G E 0.51
F E 0.65
Q E 0.66
H E 0.58
E E 0.50
T E 0.48
L C 0.49
T C 0.64
P C 0.69
R C 0.60
I H 0.54
L H 0.72
S H 0.80
Y H 0.87
Y H 0.92
G H 0.94
F H 0.95
F H 0.95
A H 0.95
F H 0.95
L H 0.95
I H 0.96
L H 0.95
V H 0.95
F H 0.94
V H 0.89
M H 0.76
K H 0.49
K C 0.64
N C 0.77
H C 0.92
END