PFRMAT SS
TARGET T0165
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0165.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0165.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0165.t2k.str.rdb  (weight 1.53983)
METHOD T0165.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 T0165.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0165
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 T0165.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 175
METHOD
METHOD ============================================
METHOD Comments from T0165.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0165
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 T0165.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 175
METHOD
METHOD ============================================
METHOD Comments from T0165.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0165
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 T0165.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 175
METHOD
METHOD ============================================
METHOD Comments from T0165.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0165
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 T0165.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 175
METHOD
METHOD ============================================
MODEL 1
M C 0.91
Q C 0.80
L C 0.72
F C 0.72
D C 0.80
L C 0.82
P C 0.82
L H 0.75
D H 0.85
Q H 0.85
L H 0.83
Q H 0.77
T H 0.71
Y H 0.55
K C 0.52
P C 0.76
E C 0.84
K C 0.86
T C 0.86
A C 0.87
P C 0.81
K C 0.63
D C 0.54
F H 0.62
S H 0.67
E H 0.71
F H 0.67
W H 0.64
K H 0.57
L H 0.52
S H 0.56
L H 0.81
E H 0.83
E H 0.82
L H 0.79
A H 0.73
K H 0.65
V H 0.47
Q C 0.56
A C 0.51
E C 0.48
P C 0.43
D C 0.41
L C 0.47
Q C 0.58
P C 0.65
V C 0.69
D C 0.78
Y C 0.81
P C 0.81
A C 0.79
D C 0.79
G C 0.73
V C 0.66
K C 0.55
V E 0.58
Y E 0.79
R E 0.89
L E 0.90
T E 0.91
Y E 0.87
K E 0.80
S C 0.63
F C 0.84
G C 0.92
N C 0.90
A C 0.54
R E 0.83
I E 0.87
T E 0.87
G E 0.90
W E 0.91
Y E 0.91
A E 0.86
V E 0.69
P C 0.65
D C 0.84
K C 0.87
E C 0.89
G C 0.88
P C 0.85
H C 0.81
P C 0.63
A E 0.90
I E 0.93
V E 0.93
K E 0.92
Y E 0.83
H C 0.52
G C 0.81
Y C 0.84
N C 0.79
A C 0.78
S C 0.79
Y C 0.73
D C 0.67
G C 0.59
E H 0.53
I H 0.71
H H 0.87
E H 0.92
M H 0.95
V H 0.95
N H 0.96
W H 0.95
A H 0.94
L H 0.87
H C 0.66
G C 0.94
Y C 0.78
A E 0.84
T E 0.93
F E 0.93
G E 0.91
M E 0.78
L C 0.66
V C 0.82
R C 0.83
G C 0.82
Q C 0.83
Q C 0.79
S C 0.81
S C 0.79
E C 0.76
D C 0.72
T C 0.62
S C 0.49
I C 0.50
S C 0.53
P C 0.59
H C 0.64
G C 0.57
H C 0.52
A H 0.47
L H 0.61
G H 0.64
W H 0.64
M H 0.66
T H 0.62
K H 0.51
G C 0.55
I C 0.61
L C 0.66
D C 0.78
K C 0.67
D C 0.70
T C 0.59
Y C 0.50
Y C 0.48
Y C 0.45
R H 0.56
G H 0.62
V H 0.78
Y H 0.92
L H 0.95
D H 0.95
A H 0.96
V H 0.96
R H 0.96
A H 0.96
L H 0.96
E H 0.96
V H 0.94
I H 0.93
S H 0.86
S H 0.64
F C 0.65
D C 0.79
E C 0.79
V C 0.81
D C 0.85
E C 0.56
T C 0.64
R C 0.52
I E 0.70
G E 0.85
V E 0.90
T E 0.80
G E 0.49
G C 0.61
S C 0.59
Q H 0.79
G H 0.91
G H 0.95
G H 0.96
L H 0.96
T H 0.96
I H 0.96
A H 0.94
A H 0.91
A H 0.78
A H 0.55
L C 0.77
S C 0.78
D C 0.71
I C 0.53
P E 0.54
K E 0.69
A E 0.84
A E 0.87
V E 0.86
A E 0.77
D E 0.57
Y C 0.62
P C 0.68
Y C 0.65
L C 0.67
S C 0.67
N C 0.48
F H 0.52
E H 0.57
R H 0.54
A H 0.49
I C 0.48
D C 0.55
V C 0.56
A C 0.56
L H 0.54
E H 0.63
Q H 0.62
P H 0.63
Y H 0.65
L H 0.63
E H 0.61
I H 0.64
N H 0.65
S H 0.63
F H 0.55
F C 0.47
R C 0.60
R C 0.59
N C 0.62
G C 0.59
S C 0.59
P C 0.61
E C 0.61
T C 0.62
E H 0.56
V H 0.76
Q H 0.78
A H 0.80
M H 0.85
K H 0.86
T H 0.85
L H 0.78
S H 0.70
Y H 0.53
F C 0.69
D C 0.83
I H 0.78
M H 0.85
N H 0.82
L H 0.76
A H 0.71
D H 0.57
R C 0.59
V C 0.80
K C 0.86
V C 0.88
P C 0.76
V E 0.87
L E 0.92
M E 0.92
S E 0.89
I E 0.62
G C 0.72
L C 0.77
I C 0.79
D C 0.82
K C 0.79
V C 0.77
T C 0.82
P C 0.86
P H 0.79
S H 0.85
T H 0.89
V H 0.93
F H 0.95
A H 0.95
A H 0.95
Y H 0.95
N H 0.95
H H 0.93
L H 0.91
E H 0.83
T H 0.64
K C 0.76
K C 0.94
E C 0.80
L E 0.68
K E 0.83
V E 0.86
Y E 0.76
R E 0.63
Y C 0.57
F C 0.75
G C 0.80
H C 0.80
E C 0.75
Y C 0.72
I C 0.71
P C 0.73
A C 0.72
F C 0.74
Q C 0.63
T C 0.60
E C 0.58
K C 0.59
L H 0.81
A H 0.91
F H 0.92
F H 0.92
K H 0.90
Q H 0.85
H H 0.74
L H 0.51
K C 0.64
G C 0.92
END