PFRMAT SS
TARGET T0399
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0399.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0399.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0399.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 T0399.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 29
METHOD
METHOD ============================================
METHOD Comments from T0399.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 29
METHOD
METHOD ============================================
METHOD Comments from T0399.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 29
METHOD
METHOD ============================================
MODEL 1
M C 0.98
S C 0.78
M C 0.57
K C 0.49
K H 0.52
T H 0.60
K H 0.76
N H 0.90
W H 0.96
L H 0.97
L H 0.97
V H 0.98
F H 0.98
L H 0.98
T H 0.98
V H 0.98
T H 0.98
F H 0.98
C H 0.97
F H 0.97
L H 0.96
M H 0.92
L H 0.82
G H 0.51
C C 0.68
Q C 0.80
S C 0.82
K C 0.81
E C 0.81
D C 0.81
K C 0.78
K C 0.75
G C 0.70
G C 0.71
T C 0.63
K C 0.59
P C 0.55
S C 0.47
N H 0.47
E H 0.53
A H 0.61
A H 0.61
L H 0.55
T H 0.52
K H 0.55
T H 0.66
E H 0.70
N H 0.71
L H 0.81
D H 0.77
F H 0.74
R H 0.59
L C 0.50
S C 0.61
F C 0.57
N C 0.60
K C 0.46
I E 0.40
K E 0.51
V E 0.47
T E 0.41
T E 0.44
D E 0.45
Q E 0.42
N C 0.42
H C 0.46
F C 0.55
S C 0.60
G C 0.78
G C 0.88
T C 0.82
S C 0.83
I H 0.95
E H 0.96
Q H 0.97
L H 0.97
K H 0.96
Q H 0.93
W H 0.88
F H 0.52
G C 0.87
D C 0.91
P C 0.82
N C 0.79
K C 0.74
S C 0.75
E C 0.76
Q C 0.70
R C 0.51
N C 0.49
A C 0.55
G C 0.82
N C 0.76
I E 0.74
T E 0.91
L E 0.95
D E 0.94
S E 0.95
Y E 0.96
T E 0.96
W E 0.93
V E 0.73
K C 0.66
D C 0.88
G C 0.83
A E 0.54
V E 0.91
I E 0.97
N E 0.98
A E 0.97
Q E 0.97
L E 0.91
Y E 0.63
K C 0.93
N C 0.94
S E 0.53
T E 0.88
V E 0.91
A E 0.89
R E 0.78
S E 0.65
I E 0.43
S C 0.64
N C 0.82
F C 0.73
S C 0.54
F C 0.57
S C 0.69
R C 0.72
E C 0.75
A C 0.79
K C 0.76
I C 0.77
G C 0.88
K H 0.89
E H 0.89
D H 0.91
Y H 0.94
D H 0.90
E H 0.87
L H 0.81
K H 0.69
I C 0.68
G C 0.94
E C 0.91
S C 0.81
Y H 0.93
K H 0.95
K H 0.96
V H 0.97
V H 0.97
E H 0.95
K H 0.92
L H 0.65
G C 0.86
E C 0.92
P C 0.84
D C 0.76
V C 0.64
L C 0.52
S C 0.46
Q E 0.40
S C 0.41
M C 0.44
S C 0.58
S C 0.80
D C 0.87
K C 0.71
E C 0.50
E E 0.73
M E 0.87
Q E 0.93
T E 0.96
V E 0.95
W E 0.95
S E 0.90
S E 0.75
G E 0.64
I E 0.68
K E 0.60
T C 0.61
K C 0.84
S C 0.86
S C 0.82
S C 0.76
A C 0.62
T E 0.69
I E 0.90
E E 0.96
L E 0.97
Y E 0.97
F E 0.95
E E 0.82
N C 0.88
G C 0.89
L E 0.61
L E 0.90
K E 0.87
N E 0.83
K E 0.58
T C 0.47
Q C 0.53
K C 0.70
D C 0.81
L C 0.89
E C 0.98
END