PFRMAT SS
TARGET YDL013W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YDL013W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YDL013W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YDL013W.t2k.str.rdb  (weight 1.53983)
METHOD YDL013W.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 YDL013W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YDL013W
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 YDL013W.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 1
METHOD
METHOD ============================================
METHOD Comments from YDL013W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YDL013W
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 YDL013W.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 1
METHOD
METHOD ============================================
METHOD Comments from YDL013W.t2k.str.rdb
METHOD ============================================
METHOD TARGET YDL013W
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 YDL013W.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 1
METHOD
METHOD ============================================
METHOD Comments from YDL013W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YDL013W
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 YDL013W.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 1
METHOD
METHOD ============================================
MODEL 1
M C 0.90
H C 0.77
S C 0.73
D C 0.76
T C 0.74
N C 0.77
G C 0.78
R C 0.69
T C 0.58
K C 0.65
S C 0.72
N C 0.79
N C 0.81
S C 0.82
P C 0.75
S C 0.74
D C 0.75
N C 0.79
N C 0.84
P C 0.80
N C 0.80
E C 0.68
T E 0.59
V E 0.83
I E 0.88
L E 0.86
I E 0.76
D C 0.57
S C 0.80
D C 0.79
K C 0.66
E C 0.58
E C 0.56
D C 0.58
A C 0.51
S C 0.44
I H 0.47
R H 0.47
E H 0.47
A C 0.57
N C 0.73
L C 0.74
P C 0.65
V E 0.53
R E 0.59
L E 0.49
Y C 0.64
P C 0.72
D C 0.75
R C 0.69
R C 0.61
V C 0.58
G C 0.64
R C 0.59
R C 0.48
R H 0.63
D H 0.65
A H 0.71
L H 0.71
N H 0.67
R H 0.66
F H 0.59
V H 0.49
R C 0.45
S C 0.57
D C 0.65
S C 0.63
R C 0.61
S C 0.64
R C 0.64
N C 0.68
S C 0.67
Q C 0.59
R C 0.50
T C 0.45
H E 0.54
I E 0.57
T E 0.49
A C 0.49
S C 0.61
S C 0.66
E C 0.70
R C 0.75
P C 0.69
D C 0.61
F C 0.52
Q C 0.55
A C 0.61
N C 0.71
N C 0.76
D C 0.74
D C 0.58
I E 0.48
T E 0.61
I E 0.60
I E 0.58
R E 0.51
E E 0.43
V H 0.34
G C 0.45
R C 0.42
F C 0.43
F C 0.59
G C 0.80
D C 0.82
D C 0.84
G C 0.87
P C 0.80
I C 0.71
D C 0.83
P C 0.69
S C 0.65
A C 0.54
H C 0.58
Y C 0.50
V C 0.48
D C 0.56
L C 0.60
D C 0.67
Q C 0.72
E C 0.79
P C 0.80
G C 0.84
S C 0.74
E C 0.64
T C 0.57
L C 0.58
E C 0.60
T C 0.68
P C 0.63
R C 0.50
T E 0.64
I E 0.71
Q E 0.75
V E 0.67
D C 0.51
N C 0.69
T C 0.72
N C 0.74
G C 0.68
Y C 0.48
L E 0.47
N C 0.60
D C 0.73
N C 0.80
G C 0.82
N C 0.78
N C 0.76
N C 0.74
E C 0.67
S C 0.67
D C 0.70
D C 0.76
G C 0.68
L E 0.51
T E 0.71
I E 0.76
V E 0.71
E E 0.63
E E 0.51
R C 0.48
T C 0.58
T C 0.64
R C 0.73
P C 0.68
R E 0.51
V E 0.71
T E 0.76
L E 0.72
N E 0.60
L C 0.71
P C 0.83
G C 0.87
G C 0.81
E C 0.59
R E 0.69
L E 0.72
E E 0.79
V E 0.78
T E 0.72
A E 0.65
T E 0.54
T C 0.50
T C 0.63
D C 0.67
I C 0.66
P C 0.63
I C 0.44
R C 0.42
R C 0.42
S C 0.43
F C 0.38
E H 0.36
F H 0.44
Q H 0.54
E H 0.58
D H 0.52
L C 0.52
G C 0.64
A C 0.48
S H 0.55
R H 0.76
R H 0.80
Q H 0.82
L H 0.82
L H 0.78
R H 0.75
R H 0.70
S H 0.62
A H 0.62
T H 0.59
R H 0.55
A H 0.54
R H 0.50
N H 0.41
L C 0.38
F E 0.44
V E 0.42
D C 0.58
R C 0.66
S C 0.71
D C 0.72
E C 0.70
N C 0.73
D C 0.70
E C 0.62
D C 0.61
W C 0.60
T C 0.61
D C 0.60
D C 0.62
T C 0.56
H C 0.57
N C 0.60
L C 0.56
P H 0.70
E H 0.83
A H 0.86
I H 0.86
Q H 0.85
R H 0.82
A H 0.77
R H 0.73
R H 0.74
E H 0.74
S H 0.71
R H 0.69
M H 0.69
R H 0.68
M H 0.73
S H 0.72
R H 0.77
R H 0.77
I H 0.81
A H 0.81
E H 0.80
R H 0.77
Q H 0.71
R H 0.69
R H 0.63
V H 0.61
Q H 0.56
Q H 0.51
Q C 0.40
R C 0.45
V C 0.54
S C 0.65
S C 0.69
D C 0.69
E C 0.67
N C 0.66
I C 0.56
S C 0.52
T C 0.37
S E 0.36
I E 0.42
R E 0.43
L H 0.52
Q H 0.63
S H 0.62
I H 0.74
R H 0.75
E H 0.76
R H 0.75
I H 0.69
Q H 0.66
S H 0.55
Y C 0.49
T C 0.67
P H 0.51
D H 0.51
I H 0.68
R H 0.72
S H 0.72
A H 0.75
F H 0.71
H H 0.64
R H 0.64
A H 0.71
E H 0.71
S H 0.71
L H 0.81
H H 0.83
E H 0.85
F H 0.86
R H 0.89
S H 0.88
I H 0.86
L H 0.83
Q H 0.75
N H 0.58
V C 0.53
A C 0.64
P C 0.56
I C 0.43
T C 0.45
L H 0.65
Q H 0.71
E H 0.70
C H 0.68
E H 0.83
E H 0.89
E H 0.90
L H 0.92
M H 0.93
A H 0.93
L H 0.93
F H 0.91
T H 0.90
E H 0.88
F H 0.86
R H 0.86
N H 0.83
Q H 0.82
L H 0.79
L H 0.77
Q H 0.76
N H 0.70
W H 0.67
A H 0.67
I H 0.72
D H 0.69
R H 0.66
V H 0.60
R H 0.58
N H 0.52
T H 0.55
Q H 0.73
E H 0.84
E H 0.85
A H 0.86
L H 0.84
R H 0.81
L H 0.79
H H 0.73
R H 0.84
E H 0.84
A H 0.84
L H 0.81
E H 0.77
R H 0.73
Q H 0.64
E H 0.56
R H 0.50
T C 0.49
A C 0.52
G C 0.61
R C 0.48
V E 0.40
F E 0.39
H C 0.46
R C 0.56
G C 0.60
T C 0.49
L H 0.42
R H 0.52
E H 0.58
S H 0.55
I H 0.55
T H 0.55
N H 0.54
Y H 0.54
L H 0.36
N C 0.47
F C 0.62
N C 0.74
G C 0.80
E C 0.69
D C 0.67
G C 0.61
F C 0.41
L H 0.47
S H 0.51
R H 0.54
L H 0.47
W C 0.42
S C 0.61
G C 0.75
P C 0.64
A C 0.57
L C 0.58
S C 0.65
D C 0.59
A C 0.50
D C 0.51
E H 0.57
E H 0.62
R H 0.59
H H 0.57
T H 0.63
Q H 0.74
N H 0.75
I H 0.86
I H 0.88
D H 0.87
M H 0.87
I H 0.84
Q H 0.80
E H 0.74
R H 0.71
E H 0.71
E H 0.72
R H 0.69
E H 0.73
R H 0.76
D H 0.76
V H 0.79
V H 0.81
M H 0.84
K H 0.83
N H 0.79
L H 0.76
M H 0.67
N H 0.55
K H 0.56
T H 0.58
R H 0.67
A H 0.70
Q H 0.71
Q H 0.78
E H 0.79
E H 0.80
F H 0.78
E H 0.79
A H 0.77
R H 0.71
A H 0.67
A H 0.55
S C 0.54
L C 0.74
P C 0.73
E C 0.67
G C 0.70
Y C 0.64
S C 0.58
A C 0.55
S C 0.59
F C 0.62
D C 0.70
T C 0.70
T C 0.76
P C 0.64
K C 0.54
M C 0.43
K E 0.52
L E 0.58
D E 0.60
I E 0.59
T C 0.51
K C 0.67
N C 0.82
G C 0.81
K C 0.65
E E 0.55
E E 0.60
T E 0.76
I E 0.86
I E 0.88
V E 0.82
T E 0.52
D C 0.71
D C 0.53
D H 0.56
L H 0.66
A H 0.67
K H 0.61
T H 0.55
L H 0.61
E H 0.53
D C 0.57
I C 0.71
P C 0.65
V E 0.51
C E 0.60
C E 0.61
L E 0.53
C C 0.52
G C 0.64
A C 0.59
E C 0.51
L C 0.55
G C 0.67
V C 0.64
G C 0.65
I C 0.68
P C 0.72
D C 0.65
D C 0.64
F C 0.60
T C 0.63
G C 0.65
I C 0.60
S C 0.56
Q C 0.51
K C 0.57
D C 0.61
R C 0.68
G C 0.74
V C 0.55
S C 0.48
F C 0.36
E H 0.40
G C 0.39
L E 0.36
V E 0.41
S E 0.35
K C 0.39
Y C 0.42
K C 0.44
F C 0.47
H C 0.59
C C 0.72
P C 0.68
Y C 0.54
Q C 0.48
T C 0.48
L C 0.52
A C 0.61
R C 0.73
P C 0.52
S C 0.48
M H 0.53
L C 0.48
D C 0.53
R H 0.49
D C 0.53
L C 0.49
S C 0.52
K H 0.50
R H 0.49
T H 0.47
F H 0.48
I H 0.45
A H 0.46
S H 0.42
C C 0.51
G C 0.60
H C 0.51
A C 0.42
F C 0.44
C C 0.48
G C 0.51
R H 0.43
C H 0.46
F H 0.47
A H 0.45
R H 0.41
I C 0.43
D C 0.49
N C 0.51
A H 0.52
K H 0.49
K C 0.48
K C 0.50
S C 0.58
K C 0.62
M C 0.73
P C 0.67
K H 0.61
K H 0.67
K H 0.68
L H 0.71
A H 0.65
Q H 0.59
L H 0.46
K C 0.58
G C 0.71
S C 0.74
A C 0.73
H C 0.79
P C 0.69
D C 0.69
N C 0.69
Y C 0.73
G C 0.80
P C 0.71
K C 0.66
L C 0.66
C C 0.79
P C 0.75
A C 0.49
D H 0.57
S H 0.60
C H 0.69
K H 0.76
K H 0.77
L H 0.75
I H 0.70
R H 0.62
S H 0.56
R C 0.51
G C 0.65
R C 0.55
L C 0.43
K C 0.44
E C 0.40
V C 0.48
Y C 0.63
F C 0.92
END