PFRMAT SS
TARGET T0642
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0642.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0642.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0642.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 T0642.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0642
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 T0642.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 1
METHOD
METHOD ============================================
METHOD Comments from T0642.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0642
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 T0642.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 1
METHOD
METHOD ============================================
METHOD Comments from T0642.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0642
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 T0642.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 1
METHOD
METHOD ============================================
MODEL 1
M C 0.95
D C 0.83
E C 0.66
A C 0.58
R C 0.58
C C 0.65
A C 0.75
S C 0.84
P C 0.75
E C 0.72
R C 0.71
S C 0.74
T C 0.68
E C 0.55
R C 0.47
R E 0.61
I E 0.80
F E 0.86
I E 0.84
C E 0.62
N C 0.61
E C 0.63
W C 0.59
S C 0.59
Y C 0.59
E C 0.59
S C 0.57
T C 0.53
E H 0.49
R H 0.55
D H 0.62
A H 0.69
Y H 0.72
W H 0.74
E H 0.77
R H 0.77
E H 0.74
L H 0.67
E H 0.56
A H 0.52
S C 0.53
E C 0.50
D C 0.52
T H 0.52
H H 0.55
E H 0.54
L H 0.51
A C 0.45
S C 0.51
T C 0.51
S C 0.45
E H 0.44
Q C 0.41
I C 0.46
N C 0.55
T C 0.55
H C 0.53
E C 0.54
N C 0.59
I C 0.58
N C 0.62
T C 0.55
H C 0.57
C C 0.63
A C 0.73
S C 0.82
P C 0.84
P C 0.74
L C 0.62
E C 0.61
A C 0.64
S C 0.70
E C 0.70
G C 0.75
E C 0.69
T C 0.64
R C 0.60
E C 0.61
S C 0.63
T C 0.61
E C 0.61
D C 0.66
A H 0.49
N C 0.53
D C 0.49
L H 0.54
E H 0.51
T H 0.50
A C 0.49
S C 0.56
S C 0.56
E H 0.48
S C 0.47
S C 0.50
M C 0.50
E C 0.56
N C 0.66
T C 0.68
D C 0.63
E H 0.55
T H 0.60
E H 0.66
R H 0.64
M H 0.59
I H 0.53
N H 0.46
E H 0.48
T C 0.49
H C 0.54
E C 0.55
E C 0.57
S C 0.60
T C 0.51
S C 0.48
C C 0.42
I C 0.39
E C 0.44
N C 0.49
T E 0.59
I E 0.83
F E 0.91
I E 0.89
C E 0.83
C E 0.54
E C 0.70
N C 0.79
T C 0.73
E C 0.67
R C 0.59
S C 0.57
T C 0.51
H C 0.43
I E 0.42
S E 0.41
T C 0.49
A C 0.60
R C 0.70
G C 0.73
E C 0.61
T C 0.47
I H 0.45
S H 0.49
D H 0.56
I H 0.50
F H 0.41
F E 0.39
E C 0.36
R C 0.46
E C 0.57
N C 0.68
T C 0.70
A C 0.67
N C 0.70
D C 0.69
H C 0.59
A C 0.51
S C 0.48
V C 0.40
E C 0.43
R C 0.52
Y C 0.67
S C 0.85
P C 0.67
E C 0.56
C E 0.51
I E 0.72
F E 0.78
I E 0.73
C E 0.46
S C 0.69
H C 0.79
A C 0.81
P C 0.60
E H 0.50
W H 0.54
I E 0.47
L E 0.61
L E 0.60
C E 0.47
H C 0.39
E C 0.46
C C 0.44
K E 0.55
I E 0.63
T E 0.55
A E 0.42
T C 0.47
T C 0.44
H H 0.48
E H 0.54
M H 0.59
E H 0.59
E H 0.58
T H 0.55
I H 0.49
N C 0.63
G C 0.79
I C 0.81
N C 0.87
P H 0.58
A H 0.66
C H 0.63
I H 0.51
F H 0.45
I H 0.45
C H 0.39
G C 0.57
R C 0.51
V C 0.41
E H 0.41
H H 0.49
A H 0.66
H H 0.65
A H 0.67
L H 0.67
A H 0.71
S H 0.72
T H 0.78
W H 0.79
C H 0.77
F H 0.80
I H 0.85
N H 0.84
A H 0.82
L H 0.76
I H 0.71
S H 0.66
T H 0.65
S H 0.58
I H 0.64
T H 0.63
A H 0.60
L H 0.55
Y H 0.49
A H 0.57
N H 0.48
D C 0.48
F H 0.45
R H 0.46
A H 0.47
N C 0.54
C C 0.55
E C 0.48
W C 0.42
E C 0.45
R H 0.47
E H 0.47
E H 0.41
L E 0.54
I E 0.63
M E 0.63
I E 0.55
N C 0.48
A C 0.62
T C 0.63
E C 0.66
D C 0.72
I C 0.78
N C 0.89
P H 0.56
R H 0.66
E H 0.72
L H 0.63
I H 0.54
M H 0.47
I H 0.48
N H 0.43
A H 0.64
R H 0.62
Y H 0.63
M H 0.60
A H 0.57
T H 0.53
C C 0.45
H C 0.58
E C 0.65
S C 0.69
S C 0.76
P C 0.57
A H 0.51
I H 0.52
N H 0.46
W H 0.41
I E 0.38
N C 0.34
A C 0.46
G C 0.61
A C 0.55
I C 0.51
N C 0.63
S C 0.71
T C 0.71
N C 0.67
E C 0.51
T H 0.49
H H 0.61
E H 0.64
R H 0.63
L H 0.60
A H 0.59
N H 0.53
D H 0.48
S H 0.53
I H 0.64
N H 0.66
F H 0.76
I H 0.80
N H 0.79
A H 0.77
L H 0.71
I H 0.63
N H 0.44
T C 0.54
E C 0.52
R C 0.50
E C 0.52
S C 0.54
T C 0.54
I C 0.59
N C 0.72
G C 0.78
E C 0.70
N C 0.66
D C 0.68
I C 0.67
N C 0.72
G C 0.67
H C 0.53
A C 0.36
V H 0.38
E H 0.45
A H 0.60
N H 0.59
I H 0.70
C H 0.72
E H 0.80
F H 0.86
A H 0.86
L H 0.84
L H 0.82
M H 0.78
E H 0.75
R H 0.73
R H 0.67
Y H 0.61
C H 0.55
H H 0.49
R H 0.49
I H 0.49
S H 0.45
T H 0.44
M H 0.41
A C 0.45
S C 0.56
A C 0.62
N C 0.71
D C 0.76
H C 0.79
A C 0.84
P C 0.84
P C 0.72
Y C 0.59
N H 0.48
E H 0.62
W H 0.66
Y H 0.66
E H 0.64
A H 0.65
R H 0.63
T H 0.60
A H 0.67
K H 0.67
E H 0.65
I H 0.59
T H 0.55
E H 0.62
A H 0.59
S H 0.50
Y C 0.47
A C 0.54
N C 0.62
D C 0.60
S C 0.53
M C 0.45
I C 0.47
L C 0.69
E C 0.98
END