PFRMAT SS
TARGET T0532
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0532.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0532.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0532.t04.str2.rdb  (weight 1.54758)
METHOD T0532.t04.alpha.rdb  (weight 0.659012)
METHOD T0532.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0532.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0532.t2k.str2.rdb  (weight 1.54758)
METHOD T0532.t2k.alpha.rdb  (weight 0.659012)
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 T0532.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0532
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	    7 (1 EBGHSTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0532.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 2107
METHOD
METHOD ============================================
METHOD Comments from T0532.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0532
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	    6 (1 EBGHTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0532.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 2107
METHOD
METHOD ============================================
METHOD Comments from T0532.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0532
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   13 (1 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0532.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 2107
METHOD
METHOD ============================================
METHOD Comments from T0532.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0532
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   11 (1 ABCDEFGHIST )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0532.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 2107
METHOD
METHOD ============================================
METHOD Comments from T0532.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0532
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 T0532.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 696
METHOD
METHOD ============================================
METHOD Comments from T0532.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0532
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 T0532.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 696
METHOD
METHOD ============================================
METHOD Comments from T0532.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0532
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.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 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0532.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 696
METHOD
METHOD ============================================
METHOD Comments from T0532.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0532
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    5	   15
METHOD	    7	   15
METHOD	    9	   15
METHOD	   13	   11 (1 ABCDEFGHIST )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0532.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 696
METHOD
METHOD ============================================
MODEL 1
M C 0.78
K H 0.59
R H 0.76
I H 0.88
N H 0.93
K H 0.95
Y H 0.95
I H 0.96
S H 0.96
L H 0.96
L H 0.96
L H 0.96
A H 0.96
T H 0.95
A H 0.95
L H 0.94
L H 0.89
A H 0.73
S C 0.58
C C 0.71
D C 0.64
K C 0.66
F H 0.60
D H 0.54
E C 0.47
I C 0.66
N C 0.83
T C 0.79
D C 0.81
P C 0.79
D C 0.81
A C 0.80
T C 0.81
T C 0.83
K H 0.55
V H 0.63
T H 0.63
S H 0.92
S H 0.93
L H 0.94
L H 0.94
A H 0.93
T H 0.92
G H 0.90
L H 0.91
L H 0.90
L H 0.85
D H 0.78
I H 0.68
T H 0.58
S H 0.51
S C 0.46
S C 0.51
A C 0.53
S C 0.54
K C 0.50
S C 0.46
F C 0.41
I C 0.39
Y C 0.37
D H 0.36
E H 0.36
L H 0.35
L E 0.34
A C 0.39
K C 0.45
Q C 0.51
M C 0.60
A C 0.65
W C 0.65
G C 0.60
E C 0.56
S C 0.52
M C 0.49
E C 0.49
D C 0.56
Y C 0.61
Q C 0.68
Y C 0.68
N C 0.67
V C 0.60
F C 0.55
G C 0.50
R H 0.54
S H 0.67
G H 0.75
F H 0.80
G H 0.81
G H 0.86
Y H 0.88
T H 0.86
T H 0.87
L H 0.90
I H 0.90
N H 0.90
A H 0.94
Q H 0.95
K H 0.95
M H 0.94
V H 0.91
E H 0.80
S H 0.58
V C 0.73
S C 0.80
D C 0.53
D C 0.52
N H 0.51
V H 0.56
N H 0.70
A H 0.78
Y H 0.89
D H 0.93
G H 0.95
L H 0.96
A H 0.96
H H 0.96
F H 0.96
I H 0.96
K H 0.96
A H 0.96
Y H 0.96
K H 0.96
I H 0.96
F H 0.96
Y H 0.95
M H 0.94
S H 0.93
M H 0.90
E H 0.84
M H 0.55
G C 0.85
D C 0.86
L C 0.73
P C 0.69
Y C 0.42
E E 0.47
E E 0.37
A C 0.44
L C 0.57
Q C 0.65
G C 0.74
E C 0.78
L C 0.75
G C 0.75
L C 0.74
V C 0.74
R C 0.80
P C 0.81
K C 0.82
Y C 0.80
N C 0.86
T C 0.70
Q H 0.92
K H 0.95
E H 0.95
V H 0.96
M H 0.96
N H 0.96
F H 0.95
I H 0.95
L H 0.95
S H 0.93
D H 0.90
L H 0.92
E H 0.94
T H 0.94
A H 0.95
Y H 0.94
E H 0.88
L H 0.76
F C 0.51
S C 0.70
T C 0.65
A C 0.71
K C 0.73
D C 0.73
F C 0.70
D C 0.63
G C 0.60
D C 0.52
P E 0.39
I E 0.41
L C 0.55
G C 0.74
G C 0.77
S C 0.64
I H 0.63
S H 0.82
K H 0.88
W H 0.93
K H 0.95
K H 0.96
A H 0.96
T H 0.96
T H 0.95
A H 0.93
F H 0.93
Q H 0.94
L H 0.94
K H 0.92
V H 0.89
L H 0.86
M H 0.85
H H 0.76
L H 0.68
S C 0.49
K C 0.69
K C 0.76
E C 0.81
S H 0.69
D H 0.76
A H 0.78
D H 0.82
L H 0.89
K H 0.92
V H 0.93
K H 0.95
E H 0.95
R H 0.95
F H 0.93
A H 0.90
R H 0.83
I H 0.76
V H 0.60
A H 0.55
S C 0.53
G C 0.68
S C 0.77
L C 0.49
M E 0.65
E E 0.62
S E 0.48
N C 0.62
E C 0.64
D C 0.63
N C 0.56
L E 0.45
Q E 0.62
M E 0.66
K E 0.57
Y C 0.47
A C 0.63
D C 0.73
K C 0.77
A C 0.76
N C 0.74
T C 0.72
V C 0.68
Y C 0.63
P C 0.55
F C 0.43
H C 0.36
N H 0.33
T E 0.36
N E 0.37
T C 0.40
K C 0.53
H C 0.62
A C 0.64
G C 0.66
Y C 0.58
A C 0.43
M H 0.38
L H 0.47
S H 0.58
T H 0.79
M H 0.81
L H 0.83
I H 0.83
D H 0.80
K H 0.76
F H 0.57
K C 0.55
A C 0.68
T C 0.74
G C 0.78
D C 0.82
I C 0.57
R C 0.55
M C 0.45
F C 0.41
Y E 0.38
Y E 0.53
A E 0.58
K E 0.49
P C 0.60
A C 0.69
K C 0.71
A C 0.69
K C 0.65
L C 0.61
N C 0.61
E C 0.61
G C 0.61
V C 0.60
T C 0.59
A C 0.60
D C 0.62
S C 0.63
W C 0.63
D C 0.63
A C 0.63
Y C 0.62
I C 0.61
G C 0.60
T C 0.60
D C 0.60
P C 0.61
S C 0.62
L C 0.60
P C 0.58
F C 0.57
E C 0.58
Q C 0.59
I C 0.57
E C 0.57
K C 0.56
A C 0.53
Y C 0.48
A C 0.47
T C 0.48
E C 0.50
Q C 0.52
Y C 0.53
S C 0.56
G C 0.58
F C 0.60
N C 0.61
A C 0.60
R C 0.60
Y C 0.59
T C 0.56
D C 0.57
Y C 0.61
P C 0.70
S C 0.75
G C 0.78
E C 0.77
P C 0.71
V C 0.51
V E 0.39
R H 0.39
L H 0.47
G H 0.60
Y H 0.93
A H 0.95
E H 0.96
Q H 0.96
N H 0.96
F H 0.96
I H 0.96
L H 0.96
A H 0.96
E H 0.96
A H 0.96
A H 0.95
V H 0.91
R H 0.75
G C 0.57
W C 0.79
I C 0.81
S C 0.78
G C 0.62
D H 0.50
A H 0.89
S H 0.93
A H 0.94
Y H 0.95
Y H 0.95
K H 0.95
K H 0.94
A H 0.93
I H 0.94
R H 0.93
A H 0.91
H H 0.86
M H 0.74
E H 0.62
F H 0.54
I C 0.48
A C 0.60
S C 0.59
N C 0.57
T C 0.47
P H 0.50
D H 0.51
E H 0.49
E H 0.43
V C 0.47
Y C 0.55
H C 0.60
H C 0.66
G C 0.60
H C 0.58
P C 0.57
I C 0.51
T C 0.50
E C 0.48
E C 0.51
A C 0.44
I H 0.46
A H 0.45
A H 0.44
F C 0.43
L C 0.44
E C 0.45
T C 0.51
P C 0.49
A C 0.49
I C 0.51
Q C 0.60
L C 0.63
S C 0.67
G C 0.69
E C 0.69
K H 0.67
E H 0.85
A H 0.89
D H 0.92
I H 0.94
E H 0.95
K H 0.95
I H 0.95
L H 0.95
T H 0.95
Q H 0.95
R H 0.95
Y H 0.94
L H 0.93
A H 0.89
S H 0.77
F H 0.59
M C 0.49
Q H 0.49
H C 0.58
P C 0.59
Y C 0.56
D H 0.48
V H 0.56
Y H 0.81
Y H 0.84
D H 0.87
Y H 0.87
R H 0.85
R H 0.76
T C 0.49
G C 0.86
Y C 0.85
P C 0.73
V C 0.63
L C 0.57
P C 0.61
I C 0.63
N C 0.67
P C 0.68
A C 0.72
T C 0.76
N C 0.77
R C 0.76
N C 0.72
T C 0.68
M C 0.73
N C 0.74
D C 0.76
R C 0.72
L C 0.69
P C 0.62
M E 0.55
R E 0.56
W C 0.54
M C 0.64
Y C 0.79
P C 0.86
K C 0.54
S H 0.56
E H 0.69
S H 0.66
D H 0.52
Y C 0.57
N C 0.77
L H 0.88
E H 0.91
H H 0.93
Q H 0.95
N H 0.96
E H 0.96
A H 0.95
L H 0.95
E H 0.93
R H 0.89
Q H 0.75
F C 0.57
G C 0.84
G C 0.88
V C 0.78
D C 0.73
D C 0.69
V C 0.69
N C 0.70
K C 0.61
L E 0.49
M E 0.62
W E 0.61
I E 0.54
L C 0.67
Q C 0.89
END