PFRMAT SS
TARGET T0390
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0390.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0390.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0390.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 T0390.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0390
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 T0390.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 117
METHOD
METHOD ============================================
METHOD Comments from T0390.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0390
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 T0390.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 117
METHOD
METHOD ============================================
METHOD Comments from T0390.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0390
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 T0390.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 117
METHOD
METHOD ============================================
MODEL 1
A C 0.84
A C 0.74
P C 0.57
E H 0.68
H H 0.68
H H 0.67
H H 0.70
H H 0.76
H H 0.91
H H 0.94
D H 0.96
Y H 0.97
D H 0.97
I H 0.97
P H 0.97
T H 0.97
T H 0.97
E H 0.96
N H 0.94
L H 0.89
Y H 0.81
F H 0.72
Q H 0.62
G H 0.58
A H 0.60
M H 0.64
D H 0.56
A H 0.47
A C 0.42
D C 0.50
R C 0.61
H C 0.59
T E 0.68
V E 0.84
F E 0.84
W E 0.72
N C 0.62
S C 0.80
S C 0.85
N C 0.85
P C 0.65
K C 0.46
F C 0.37
R C 0.46
N C 0.70
E C 0.89
D C 0.89
Y E 0.58
T E 0.91
I E 0.94
H E 0.93
V E 0.83
Q E 0.66
L C 0.65
N C 0.79
D C 0.69
Y C 0.52
V E 0.66
D E 0.69
I E 0.82
I E 0.82
C E 0.63
P C 0.59
H C 0.75
Y C 0.84
E C 0.89
D C 0.90
H C 0.90
S C 0.88
V C 0.88
A C 0.89
D C 0.85
A C 0.86
A C 0.72
M C 0.49
E E 0.73
Q E 0.91
Y E 0.95
I E 0.97
L E 0.97
Y E 0.96
L E 0.92
V E 0.69
E C 0.71
H H 0.73
E H 0.78
E H 0.82
Y H 0.79
Q H 0.62
L H 0.45
C C 0.61
Q C 0.67
P C 0.63
Q C 0.74
S C 0.78
K C 0.82
D C 0.85
Q C 0.69
V E 0.56
R E 0.82
W E 0.87
Q E 0.81
C C 0.51
N C 0.81
R C 0.90
P C 0.87
S C 0.86
A C 0.91
K C 0.90
H C 0.86
G C 0.87
P C 0.71
E C 0.55
K C 0.42
L E 0.46
S E 0.52
E E 0.56
K E 0.51
F E 0.53
Q E 0.56
R E 0.58
F E 0.49
T C 0.71
P C 0.78
F C 0.86
T C 0.82
L C 0.84
G C 0.75
K C 0.58
E E 0.57
F E 0.63
K C 0.64
E C 0.93
G C 0.96
H C 0.76
S E 0.61
Y E 0.95
Y E 0.98
Y E 0.98
I E 0.96
S E 0.81
K C 0.62
P C 0.85
I C 0.92
H C 0.90
Q C 0.88
H C 0.73
E C 0.69
D C 0.63
R C 0.53
C C 0.46
L C 0.47
R C 0.58
L C 0.75
K C 0.78
V C 0.50
T E 0.85
V E 0.90
S E 0.87
G E 0.53
K C 0.85
I C 0.89
T C 0.78
H C 0.65
S E 0.69
P E 0.81
Q E 0.83
A E 0.79
H E 0.63
V C 0.62
N C 0.80
P C 0.91
Q C 0.87
E C 0.86
K C 0.86
R C 0.86
L C 0.86
A C 0.83
A C 0.85
D C 0.87
D C 0.92
P C 0.97
END