PFRMAT SS
TARGET T0443
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0443.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0443.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0443.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 T0443.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0443
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 T0443.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 56
METHOD
METHOD ============================================
METHOD Comments from T0443.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0443
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 T0443.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 56
METHOD
METHOD ============================================
METHOD Comments from T0443.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0443
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 T0443.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 56
METHOD
METHOD ============================================
MODEL 1
M C 0.98
Q C 0.96
P C 0.90
E H 0.73
T H 0.77
S H 0.89
A H 0.94
Q H 0.95
Y H 0.96
Q H 0.97
H H 0.97
R H 0.97
F H 0.97
S H 0.97
Q H 0.94
A H 0.91
I H 0.82
R H 0.60
G C 0.82
G C 0.88
E C 0.89
A C 0.89
A C 0.91
D C 0.91
G C 0.92
L C 0.86
P C 0.60
Q H 0.89
D H 0.91
R H 0.94
L H 0.96
N H 0.96
V H 0.95
Y H 0.96
I H 0.97
R H 0.97
L H 0.95
I H 0.95
R H 0.93
N H 0.89
N H 0.87
I H 0.94
H H 0.94
S H 0.94
F H 0.95
I H 0.92
D H 0.83
R H 0.70
C H 0.56
Y C 0.54
T H 0.62
E H 0.68
T H 0.67
R H 0.76
Q H 0.70
Y H 0.51
F C 0.82
D C 0.93
S H 0.84
K H 0.93
E H 0.94
W H 0.96
S H 0.97
R H 0.97
L H 0.96
K H 0.97
E H 0.97
G H 0.97
F H 0.96
V H 0.95
R H 0.91
D H 0.77
A C 0.60
R C 0.77
A C 0.82
Q C 0.84
T C 0.88
P H 0.57
Y H 0.66
F H 0.82
Q H 0.87
E H 0.86
I H 0.90
P H 0.95
G H 0.96
E H 0.97
F H 0.97
L H 0.97
Q H 0.97
Y H 0.95
C H 0.91
Q H 0.78
S C 0.55
P C 0.73
P C 0.85
L C 0.88
S C 0.81
D H 0.74
G H 0.79
I H 0.93
L H 0.94
A H 0.94
L H 0.93
M H 0.91
D H 0.89
F H 0.91
E H 0.92
Y H 0.93
T H 0.94
Q H 0.95
L H 0.92
L H 0.87
A H 0.79
E H 0.71
V H 0.60
A C 0.46
Q C 0.66
I C 0.78
P C 0.84
D C 0.86
I C 0.88
P C 0.88
D C 0.85
I C 0.63
H C 0.60
Y C 0.57
S C 0.53
N C 0.60
D C 0.70
S C 0.80
K C 0.75
Y C 0.65
T C 0.62
P C 0.65
S C 0.85
P H 0.65
A H 0.69
A H 0.64
F H 0.62
I H 0.62
R H 0.55
Q H 0.46
Y C 0.56
R C 0.70
Y C 0.72
D C 0.54
V E 0.57
T E 0.61
H E 0.53
D C 0.59
L C 0.80
Q C 0.85
E C 0.86
A C 0.88
E C 0.89
T E 0.59
A E 0.92
L E 0.97
L E 0.98
I E 0.97
W E 0.95
R E 0.84
N C 0.69
A C 0.91
E C 0.90
D C 0.81
D C 0.49
V E 0.87
M E 0.89
Y E 0.87
Q E 0.82
T E 0.65
L C 0.73
D C 0.86
G H 0.93
F H 0.96
D H 0.97
M H 0.98
M H 0.97
L H 0.97
L H 0.97
E H 0.96
I H 0.94
M H 0.92
G H 0.84
S H 0.71
S H 0.50
A C 0.56
L C 0.56
S C 0.52
F H 0.66
D H 0.83
T H 0.90
L H 0.93
A H 0.95
Q H 0.96
T H 0.95
L H 0.95
V H 0.93
E H 0.88
F H 0.79
M H 0.63
P H 0.56
K H 0.55
A H 0.50
D C 0.54
N C 0.53
W H 0.84
K H 0.92
N H 0.93
I H 0.94
L H 0.93
L H 0.92
G H 0.87
K H 0.85
W H 0.83
S H 0.83
G H 0.76
W H 0.68
I H 0.60
E H 0.57
Q H 0.53
R H 0.40
I E 0.54
I E 0.58
I C 0.50
P C 0.76
S C 0.85
L C 0.73
S C 0.70
A C 0.59
I C 0.63
S C 0.70
E C 0.75
N C 0.82
M C 0.81
E C 0.83
G C 0.86
N C 0.90
S C 0.88
P C 0.76
S C 0.71
Q C 0.58
N C 0.58
H C 0.54
L C 0.64
S C 0.75
A C 0.79
END