PFRMAT SS
TARGET T0393
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0393.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0393.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0393.t2k.str.rdb  (weight 1.53983)
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 T0393.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 640
METHOD
METHOD ============================================
METHOD Comments from T0393.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 640
METHOD
METHOD ============================================
METHOD Comments from T0393.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 640
METHOD
METHOD ============================================
MODEL 1
M C 0.91
K C 0.79
R C 0.81
S C 0.83
I C 0.54
E C 0.63
D C 0.76
T C 0.88
P C 0.59
I E 0.95
V E 0.98
L E 0.98
I E 0.95
G E 0.57
A C 0.81
G C 0.62
N H 0.93
L H 0.96
A H 0.97
T H 0.97
N H 0.97
L H 0.98
A H 0.98
K H 0.97
A H 0.97
L H 0.97
Y H 0.96
R H 0.90
K C 0.65
G C 0.98
F C 0.95
R E 0.53
I E 0.96
V E 0.98
Q E 0.98
V E 0.95
Y E 0.80
S C 0.62
R C 0.91
T C 0.94
E H 0.89
E H 0.92
S H 0.95
A H 0.97
R H 0.96
E H 0.96
L H 0.96
A H 0.96
Q H 0.92
K H 0.85
V H 0.53
E C 0.92
A C 0.91
E C 0.68
Y C 0.56
T C 0.60
T C 0.76
D C 0.81
L H 0.83
A H 0.91
E H 0.91
V H 0.90
N H 0.83
P H 0.52
Y C 0.74
A C 0.94
K C 0.91
L E 0.96
Y E 0.98
I E 0.98
V E 0.98
S E 0.77
L C 0.66
K C 0.85
D C 0.72
S H 0.52
A H 0.71
F H 0.84
A H 0.90
E H 0.91
L H 0.93
L H 0.93
Q H 0.91
G H 0.86
I H 0.79
V H 0.75
E H 0.68
G H 0.59
K C 0.56
R C 0.72
E C 0.86
E C 0.94
A C 0.70
L E 0.87
M E 0.96
V E 0.97
H E 0.94
T E 0.71
A C 0.67
G C 0.80
S C 0.79
I C 0.79
P C 0.83
M H 0.63
N H 0.70
V H 0.76
W H 0.76
E H 0.78
G H 0.80
H H 0.80
V H 0.72
P H 0.55
H C 0.64
Y C 0.87
G C 0.84
V E 0.51
F E 0.80
Y E 0.82
P E 0.75
M E 0.54
Q C 0.71
T C 0.82
F C 0.82
S C 0.81
K C 0.67
Q C 0.48
R H 0.61
E H 0.66
V H 0.64
D H 0.57
F C 0.48
K C 0.61
E C 0.66
I C 0.53
P E 0.45
F E 0.62
F E 0.62
I E 0.44
E C 0.55
A C 0.78
S C 0.91
S C 0.92
T H 0.91
E H 0.94
D H 0.96
A H 0.97
A H 0.97
F H 0.96
L H 0.97
K H 0.97
A H 0.97
I H 0.97
A H 0.96
S H 0.93
T H 0.79
L H 0.53
S C 0.90
N C 0.88
R C 0.62
V E 0.70
Y E 0.87
D E 0.85
A E 0.50
D C 0.87
S C 0.62
E C 0.58
Q H 0.55
R H 0.60
K H 0.64
S H 0.68
L H 0.72
H H 0.79
L H 0.85
A H 0.88
A H 0.90
V H 0.82
F H 0.73
T H 0.81
C H 0.93
N H 0.96
F H 0.97
T H 0.97
N H 0.98
H H 0.98
M H 0.98
Y H 0.98
A H 0.98
L H 0.97
A H 0.97
A H 0.97
E H 0.97
L H 0.97
L H 0.97
K H 0.96
K H 0.88
Y C 0.60
N C 0.98
L C 0.97
P C 0.97
F H 0.87
D H 0.91
V H 0.92
M H 0.94
L H 0.95
P H 0.96
L H 0.96
I H 0.97
D H 0.96
E H 0.94
T H 0.93
A H 0.91
R H 0.89
K H 0.77
V H 0.79
H H 0.82
E H 0.75
L H 0.63
E C 0.66
P C 0.63
K C 0.53
T C 0.55
A C 0.60
Q C 0.68
T C 0.75
G C 0.81
P C 0.72
A C 0.51
I C 0.48
R C 0.62
Y C 0.81
D C 0.78
E H 0.94
N H 0.97
V H 0.97
I H 0.98
G H 0.98
N H 0.97
H H 0.97
L H 0.97
R H 0.96
M H 0.94
L H 0.90
A H 0.78
D H 0.61
D C 0.54
P C 0.66
A H 0.73
M H 0.81
Q H 0.86
R H 0.91
L H 0.93
Y H 0.94
E H 0.93
L H 0.92
L H 0.88
S H 0.84
R H 0.80
S H 0.74
I H 0.69
H H 0.55
E C 0.54
R C 0.76
Q C 0.95
END