PFRMAT SS
TARGET T0478
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0478.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0478.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0478.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 T0478.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0478
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 T0478.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 43
METHOD
METHOD ============================================
METHOD Comments from T0478.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0478
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 T0478.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 43
METHOD
METHOD ============================================
METHOD Comments from T0478.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0478
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 T0478.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 43
METHOD
METHOD ============================================
MODEL 1
M C 0.96
S C 0.88
L C 0.85
D C 0.85
T C 0.79
G C 0.76
V C 0.75
T C 0.74
S H 0.52
V H 0.75
M H 0.85
F H 0.89
V H 0.89
E H 0.92
R H 0.92
S H 0.92
L H 0.95
N H 0.95
E H 0.95
I H 0.96
R H 0.96
F H 0.97
W H 0.97
S H 0.97
R H 0.97
I H 0.97
M H 0.97
K H 0.96
E H 0.96
H H 0.96
S H 0.96
F H 0.97
F H 0.97
L H 0.96
R H 0.95
L H 0.82
G H 0.55
F C 0.87
R C 0.95
C H 0.65
E H 0.71
D H 0.79
T H 0.75
Q H 0.66
L H 0.80
I H 0.94
E H 0.95
E H 0.96
A H 0.97
N H 0.96
Q H 0.95
F H 0.96
Y H 0.96
R H 0.95
L H 0.95
F H 0.96
E H 0.96
H H 0.96
I H 0.96
E H 0.96
Q H 0.94
I H 0.92
A H 0.88
H H 0.75
S H 0.63
Y C 0.51
T C 0.73
N C 0.85
E C 0.87
T C 0.84
D C 0.83
P C 0.60
E H 0.64
Q H 0.73
I H 0.85
K H 0.85
R H 0.83
F H 0.86
N H 0.89
A H 0.97
E H 0.97
V H 0.97
Q H 0.97
Q H 0.97
A H 0.97
A H 0.97
T H 0.97
N H 0.96
I H 0.96
W H 0.96
G H 0.94
F H 0.94
K H 0.95
R H 0.95
K H 0.94
I H 0.95
L H 0.95
G H 0.93
L H 0.88
I H 0.85
L H 0.73
T H 0.57
C C 0.53
K C 0.55
L C 0.54
P C 0.61
G C 0.71
Q C 0.84
N C 0.90
N C 0.85
F C 0.82
P H 0.55
L H 0.62
L H 0.77
V H 0.90
D H 0.96
H H 0.96
T H 0.97
S H 0.97
R H 0.97
E H 0.97
A H 0.97
D H 0.98
Y H 0.97
F H 0.97
R H 0.97
K H 0.97
R H 0.97
L H 0.97
I H 0.96
Q H 0.94
L H 0.92
N H 0.78
E C 0.57
G C 0.90
K C 0.90
L C 0.79
D C 0.89
A C 0.80
L C 0.69
P C 0.54
D H 0.57
A H 0.63
I H 0.75
I H 0.78
K H 0.81
E H 0.82
N H 0.85
V H 0.86
F H 0.85
F H 0.88
L H 0.93
R H 0.95
I H 0.95
M H 0.95
A H 0.95
D H 0.93
H H 0.91
A H 0.90
K H 0.88
F H 0.87
I H 0.85
G H 0.83
H H 0.76
L H 0.59
L C 0.71
D C 0.85
P H 0.74
S H 0.83
E H 0.95
R H 0.96
K H 0.97
L H 0.97
V H 0.97
D H 0.97
T H 0.96
A H 0.96
R H 0.96
N H 0.94
F H 0.94
S H 0.95
N H 0.93
D H 0.93
F H 0.95
D H 0.95
E H 0.96
L H 0.97
M H 0.97
Y H 0.97
Q H 0.96
A H 0.96
I H 0.95
D H 0.92
L H 0.91
E H 0.86
S H 0.75
M H 0.66
K H 0.49
P C 0.58
Q C 0.68
S C 0.70
Q C 0.76
T C 0.73
A C 0.57
P H 0.65
L H 0.72
L H 0.85
D H 0.84
Q H 0.82
F H 0.85
L H 0.88
D H 0.93
Q H 0.94
N H 0.96
R H 0.97
V H 0.97
S H 0.97
V H 0.97
A H 0.97
S H 0.96
L H 0.96
R H 0.97
D H 0.96
F H 0.96
K H 0.97
K H 0.96
T H 0.96
A H 0.96
R H 0.95
D H 0.93
L H 0.91
I H 0.93
E H 0.93
Q H 0.90
C H 0.85
K H 0.85
I H 0.85
K H 0.88
S H 0.86
I H 0.84
I H 0.85
H H 0.84
P H 0.81
L H 0.72
L H 0.69
A H 0.77
D H 0.76
H H 0.78
V H 0.81
F H 0.82
R H 0.84
E H 0.86
A H 0.92
D H 0.94
R H 0.95
F H 0.97
L H 0.97
E H 0.97
I H 0.97
I H 0.96
D H 0.92
M H 0.88
Y H 0.83
D H 0.70
V H 0.52
H C 0.65
L C 0.83
T C 0.90
N C 0.84
I C 0.81
Q C 0.80
S C 0.91
Q C 0.91
P C 0.90
R C 0.92
E C 0.90
G C 0.89
H C 0.84
H C 0.75
H C 0.75
H C 0.79
H C 0.87
H C 0.98
END