PFRMAT SS
TARGET T0528
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0528.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0528.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0528.t04.str2.rdb  (weight 1.54758)
METHOD T0528.t04.alpha.rdb  (weight 0.659012)
METHOD T0528.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0528.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0528.t2k.str2.rdb  (weight 1.54758)
METHOD T0528.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 T0528.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0528
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 T0528.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 1749
METHOD
METHOD ============================================
METHOD Comments from T0528.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0528
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 T0528.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 1749
METHOD
METHOD ============================================
METHOD Comments from T0528.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0528
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 T0528.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 1749
METHOD
METHOD ============================================
METHOD Comments from T0528.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0528
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 T0528.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 1749
METHOD
METHOD ============================================
METHOD Comments from T0528.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0528
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 T0528.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 2130
METHOD
METHOD ============================================
METHOD Comments from T0528.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0528
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 T0528.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 2130
METHOD
METHOD ============================================
METHOD Comments from T0528.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0528
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 T0528.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 2130
METHOD
METHOD ============================================
METHOD Comments from T0528.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0528
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 T0528.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 2130
METHOD
METHOD ============================================
MODEL 1
M H 0.87
T H 0.92
A H 0.92
T H 0.92
A H 0.91
V H 0.90
A H 0.86
L H 0.81
A H 0.72
T H 0.68
T H 0.66
A H 0.64
V H 0.58
H H 0.51
A C 0.60
A C 0.80
D C 0.86
D C 0.64
L E 0.79
K E 0.89
I E 0.90
A E 0.89
L E 0.90
I E 0.83
Y E 0.64
G C 0.59
K C 0.71
T C 0.75
G C 0.78
P C 0.55
L H 0.57
E H 0.64
A H 0.59
Y H 0.51
A C 0.49
K H 0.78
Q H 0.85
T H 0.93
E H 0.95
T H 0.95
G H 0.96
L H 0.96
M H 0.96
M H 0.96
G H 0.96
L H 0.96
E H 0.96
Y H 0.95
A H 0.93
T H 0.88
K H 0.74
G C 0.60
T C 0.81
M C 0.78
T C 0.61
L C 0.58
D C 0.79
G C 0.86
R C 0.66
K E 0.69
I E 0.84
V E 0.89
V E 0.91
I E 0.89
T E 0.83
K E 0.59
D C 0.77
D C 0.84
Q C 0.87
S C 0.89
K C 0.88
P H 0.88
D H 0.94
L H 0.95
S H 0.96
K H 0.96
A H 0.96
A H 0.96
L H 0.96
A H 0.96
E H 0.95
A H 0.94
Y H 0.93
Q H 0.86
D H 0.55
D C 0.76
G C 0.90
A C 0.74
D E 0.60
I E 0.92
A E 0.93
I E 0.88
G E 0.75
T C 0.69
S C 0.83
S C 0.81
S C 0.65
A H 0.80
A H 0.87
A H 0.91
L H 0.93
A H 0.91
D H 0.91
L H 0.93
P H 0.95
V H 0.96
A H 0.95
E H 0.94
E H 0.85
N C 0.61
K C 0.94
K C 0.88
I E 0.51
L E 0.84
I E 0.88
V E 0.81
E E 0.60
P C 0.72
A C 0.80
V C 0.82
A C 0.76
D C 0.61
Q C 0.51
I C 0.52
T C 0.63
G C 0.72
E C 0.73
K C 0.77
W C 0.78
N C 0.83
R C 0.79
Y C 0.59
I E 0.77
F E 0.85
R E 0.83
T E 0.68
G C 0.65
R C 0.84
N C 0.89
S H 0.60
S H 0.85
Q H 0.90
D H 0.90
A H 0.93
I H 0.95
S H 0.95
N H 0.95
A H 0.95
V H 0.95
A H 0.94
I H 0.91
G H 0.81
K C 0.67
Q C 0.90
G C 0.91
V C 0.81
T E 0.82
I E 0.93
A E 0.93
T E 0.93
L E 0.86
A C 0.50
Q C 0.81
D C 0.86
Y C 0.77
A C 0.54
F C 0.49
G H 0.60
R H 0.83
D H 0.88
G H 0.92
V H 0.95
A H 0.95
A H 0.96
F H 0.96
K H 0.96
E H 0.96
A H 0.96
L H 0.96
A H 0.94
K H 0.87
T C 0.65
G C 0.94
A C 0.86
T E 0.72
L E 0.87
A E 0.86
T E 0.82
E E 0.77
E E 0.76
Y E 0.72
V E 0.54
P C 0.75
T C 0.85
T C 0.89
T C 0.79
T C 0.72
D C 0.66
F H 0.82
T H 0.91
A H 0.94
V H 0.95
G H 0.94
Q H 0.92
R H 0.91
L H 0.91
F H 0.90
D H 0.86
A H 0.80
L H 0.72
K H 0.56
D C 0.64
K C 0.89
P C 0.89
G C 0.75
K E 0.92
K E 0.93
I E 0.93
I E 0.90
W E 0.60
V C 0.75
I C 0.82
W C 0.77
A H 0.60
G H 0.72
G H 0.89
G H 0.94
D H 0.95
P H 0.96
L H 0.96
T H 0.96
K H 0.96
L H 0.96
Q H 0.95
D H 0.91
M C 0.54
D C 0.94
P C 0.91
K C 0.84
R C 0.70
Y E 0.53
G E 0.79
I E 0.80
E E 0.72
L E 0.58
S C 0.53
T C 0.63
G C 0.66
G C 0.70
N C 0.74
I H 0.86
L H 0.91
P H 0.93
A H 0.93
L H 0.91
A H 0.86
A H 0.69
Y H 0.51
K H 0.59
R H 0.59
L H 0.47
P C 0.60
G C 0.71
M C 0.50
E E 0.76
G E 0.82
A E 0.74
T E 0.55
Y C 0.57
Y C 0.64
Y C 0.68
Y C 0.70
D C 0.69
I C 0.74
P C 0.78
K C 0.82
N C 0.84
P H 0.79
I H 0.84
N H 0.91
E H 0.95
W H 0.96
L H 0.96
V H 0.96
T H 0.96
E H 0.96
H H 0.96
Q H 0.95
K H 0.92
R H 0.84
F H 0.53
N C 0.88
A C 0.87
P C 0.89
P C 0.81
D C 0.78
F H 0.62
F H 0.79
T H 0.87
A H 0.93
G H 0.93
G H 0.95
F H 0.96
S H 0.96
A H 0.96
A H 0.96
M H 0.96
A H 0.96
V H 0.96
V H 0.96
T H 0.96
A H 0.96
V H 0.95
Q H 0.93
K H 0.85
A C 0.52
K C 0.91
S C 0.89
T C 0.86
D C 0.85
T H 0.89
E H 0.95
K H 0.96
L H 0.96
I H 0.96
A H 0.95
A H 0.93
M H 0.90
E H 0.70
G C 0.70
M C 0.85
E C 0.77
F C 0.68
D C 0.69
T C 0.75
P C 0.76
K C 0.76
G C 0.73
K C 0.56
M E 0.78
V E 0.85
F E 0.84
R E 0.51
K C 0.80
E C 0.87
D C 0.88
H C 0.84
Q C 0.54
A E 0.53
L E 0.49
Q C 0.55
S E 0.54
M E 0.81
Y E 0.91
H E 0.93
F E 0.92
K E 0.92
V E 0.89
K E 0.72
V C 0.68
D C 0.89
P C 0.83
A E 0.51
V E 0.79
A E 0.82
W E 0.78
A E 0.66
V C 0.49
L C 0.53
E C 0.57
P C 0.59
V C 0.49
R E 0.51
E C 0.60
L C 0.77
K C 0.80
I C 0.83
E C 0.73
E C 0.57
M C 0.46
N C 0.51
I C 0.66
P C 0.77
I C 0.80
K C 0.77
N C 0.79
K C 0.81
K C 0.89
END