PFRMAT SS
TARGET T0159
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0159.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0159.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0159.t2k.str.rdb  (weight 1.53983)
METHOD T0159.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 T0159.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0159
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 T0159.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 45
METHOD
METHOD ============================================
METHOD Comments from T0159.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0159
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 T0159.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 45
METHOD
METHOD ============================================
METHOD Comments from T0159.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0159
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 T0159.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 45
METHOD
METHOD ============================================
METHOD Comments from T0159.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0159
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 T0159.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 45
METHOD
METHOD ============================================
MODEL 1
A C 0.73
D C 0.71
L C 0.74
P C 0.63
G C 0.63
K C 0.67
G C 0.84
I C 0.81
T E 0.53
V E 0.76
N E 0.84
P E 0.83
V E 0.74
Q E 0.52
S C 0.74
T C 0.83
I H 0.55
T H 0.68
E H 0.85
E H 0.91
T H 0.92
F H 0.94
Q H 0.95
T H 0.95
L H 0.96
L H 0.96
V H 0.96
S H 0.96
R H 0.96
A H 0.96
L H 0.96
E H 0.94
K H 0.89
L C 0.55
G C 0.93
Y C 0.88
T C 0.71
V C 0.58
N C 0.54
K E 0.54
P C 0.52
S C 0.50
E C 0.51
V C 0.67
D C 0.69
Y C 0.51
N H 0.45
V H 0.62
G H 0.70
Y H 0.75
T H 0.77
S H 0.79
L H 0.80
A H 0.76
S C 0.56
G C 0.90
D C 0.84
A C 0.52
T E 0.50
F E 0.70
T E 0.68
A E 0.38
V H 0.50
N H 0.52
W C 0.44
T C 0.62
P C 0.60
L C 0.63
H C 0.64
D H 0.56
N H 0.83
M H 0.87
Y H 0.89
E H 0.89
A H 0.88
A H 0.84
G H 0.71
G H 0.53
D C 0.67
K C 0.85
K C 0.69
F E 0.65
Y E 0.69
R E 0.69
E E 0.54
G C 0.54
V C 0.52
F C 0.59
V C 0.67
N C 0.71
G C 0.71
A C 0.49
A E 0.62
Q E 0.74
G E 0.77
Y E 0.82
L E 0.77
I E 0.56
D C 0.67
K H 0.59
K H 0.67
T H 0.72
A H 0.60
D C 0.51
Q C 0.80
Y C 0.85
K C 0.89
I C 0.78
T C 0.75
N C 0.79
I H 0.77
A H 0.75
Q H 0.76
L H 0.66
K H 0.51
D C 0.60
P C 0.63
K C 0.57
I H 0.45
A C 0.47
K C 0.47
L C 0.65
F C 0.71
D C 0.82
T C 0.75
N C 0.77
G C 0.76
D C 0.75
G C 0.77
K C 0.76
A C 0.61
D E 0.54
L E 0.66
T E 0.50
G C 0.64
C C 0.76
N C 0.80
P C 0.80
G C 0.78
W C 0.66
G C 0.54
C H 0.73
E H 0.81
G H 0.89
A H 0.92
I H 0.94
N H 0.95
H H 0.94
Q H 0.94
L H 0.93
A H 0.91
A H 0.81
Y C 0.51
E C 0.83
L C 0.82
T C 0.80
N C 0.82
T C 0.77
V E 0.69
T E 0.85
H E 0.84
N E 0.66
Q C 0.63
G C 0.85
N C 0.79
Y H 0.76
A H 0.91
A H 0.93
M H 0.95
M H 0.95
A H 0.96
D H 0.95
T H 0.95
I H 0.95
S H 0.95
R H 0.94
Y H 0.90
K H 0.68
E C 0.72
G C 0.94
K C 0.92
P C 0.72
V E 0.82
F E 0.92
Y E 0.92
Y E 0.88
T E 0.74
W C 0.51
T C 0.75
P C 0.73
Y C 0.61
W C 0.45
V H 0.50
S H 0.57
N C 0.49
E C 0.54
L C 0.68
K C 0.88
P C 0.87
G C 0.88
K C 0.75
D C 0.61
V E 0.44
V E 0.45
W E 0.47
L C 0.57
Q C 0.69
V C 0.81
P C 0.81
F C 0.73
S C 0.69
A C 0.72
L C 0.77
P C 0.78
G C 0.72
D C 0.69
K C 0.68
N C 0.70
A C 0.65
D C 0.64
T C 0.66
K C 0.74
L C 0.78
P C 0.77
N C 0.76
G C 0.68
A C 0.60
N C 0.57
Y C 0.65
G C 0.75
F C 0.77
P C 0.76
V H 0.48
S H 0.64
T H 0.68
M H 0.70
H H 0.72
I H 0.73
V H 0.73
A H 0.74
N H 0.69
K H 0.76
A H 0.73
W H 0.80
A H 0.86
E H 0.77
K H 0.72
N C 0.63
P H 0.80
A H 0.87
A H 0.94
A H 0.95
K H 0.95
L H 0.95
F H 0.94
A H 0.91
I H 0.72
M C 0.62
Q C 0.88
L C 0.88
P C 0.92
V H 0.83
A H 0.90
D H 0.91
I H 0.94
N H 0.93
A H 0.94
Q H 0.94
N H 0.95
A H 0.95
I H 0.95
M H 0.94
H H 0.87
A H 0.57
G C 0.71
A C 0.75
A C 0.76
S C 0.80
E C 0.79
G C 0.80
D C 0.81
I H 0.90
Q H 0.94
G H 0.95
H H 0.95
V H 0.96
D H 0.96
G H 0.96
W H 0.96
I H 0.95
K H 0.93
A H 0.83
H H 0.49
Q H 0.88
Q H 0.88
Q H 0.87
F H 0.85
D H 0.83
G H 0.80
W H 0.68
V C 0.47
N C 0.53
E H 0.86
A H 0.86
L H 0.85
A H 0.76
A H 0.59
Q C 0.61
K C 0.91
END