PFRMAT SS
TARGET T0573
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0573.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0573.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0573.t04.str2.rdb  (weight 1.54758)
METHOD T0573.t04.alpha.rdb  (weight 0.659012)
METHOD T0573.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0573.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0573.t2k.str2.rdb  (weight 1.54758)
METHOD T0573.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 T0573.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0573
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 T0573.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 276.896
METHOD
METHOD ============================================
METHOD Comments from T0573.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0573
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 T0573.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 276.896
METHOD
METHOD ============================================
METHOD Comments from T0573.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0573
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 T0573.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 276.896
METHOD
METHOD ============================================
METHOD Comments from T0573.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0573
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 T0573.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 276.896
METHOD
METHOD ============================================
METHOD Comments from T0573.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0573
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 T0573.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 2495
METHOD
METHOD ============================================
METHOD Comments from T0573.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0573
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 T0573.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 2495
METHOD
METHOD ============================================
METHOD Comments from T0573.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0573
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 T0573.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 2495
METHOD
METHOD ============================================
METHOD Comments from T0573.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0573
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 T0573.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 2495
METHOD
METHOD ============================================
MODEL 1
M C 0.85
S C 0.76
T C 0.68
S C 0.55
A E 0.79
I E 0.82
D E 0.64
P C 0.58
V C 0.56
S H 0.56
F C 0.56
S C 0.71
L C 0.80
Y C 0.82
A C 0.73
K H 0.56
D H 0.62
F H 0.79
T H 0.92
R H 0.95
F H 0.95
A H 0.96
Q H 0.96
E H 0.96
L H 0.96
G H 0.96
A H 0.95
S H 0.94
F H 0.93
E H 0.88
R H 0.74
Y C 0.64
G C 0.87
F C 0.52
A E 0.78
V E 0.88
L E 0.87
S E 0.74
D C 0.48
Y C 0.79
D C 0.83
L C 0.84
D C 0.91
Q H 0.91
A H 0.94
R H 0.95
I H 0.96
D H 0.95
A H 0.95
A H 0.95
V H 0.96
D H 0.95
S H 0.95
A H 0.95
K H 0.93
A H 0.90
F H 0.83
F H 0.66
A C 0.58
L C 0.86
P C 0.89
V H 0.87
E H 0.89
T H 0.91
K H 0.90
K H 0.86
Q H 0.81
Y H 0.68
A H 0.50
G C 0.61
V C 0.71
K C 0.75
G C 0.75
G C 0.74
A C 0.71
R C 0.65
G C 0.57
Y C 0.48
I E 0.48
P C 0.49
F C 0.56
G C 0.59
V C 0.57
E C 0.54
T C 0.51
A C 0.53
K C 0.62
G C 0.68
A C 0.72
D C 0.73
H C 0.70
Y C 0.64
D C 0.62
L H 0.47
K H 0.49
E H 0.49
F H 0.42
W C 0.43
H C 0.52
M C 0.51
G C 0.57
R C 0.56
D C 0.59
L C 0.65
P C 0.64
P C 0.63
G C 0.66
H C 0.67
R C 0.69
F C 0.66
R C 0.61
A C 0.61
H C 0.65
M C 0.68
A C 0.72
D C 0.70
N C 0.71
V C 0.69
W C 0.74
P C 0.65
A C 0.65
E C 0.74
I C 0.75
P H 0.70
A H 0.70
F H 0.84
K H 0.93
H H 0.95
D H 0.95
V H 0.95
S H 0.96
W H 0.96
L H 0.96
Y H 0.96
N H 0.96
S H 0.95
L H 0.95
D H 0.96
G H 0.95
M H 0.95
G H 0.96
G H 0.96
K H 0.96
V H 0.96
L H 0.96
E H 0.96
A H 0.96
I H 0.96
A H 0.96
T H 0.94
Y H 0.85
L C 0.52
K C 0.91
L C 0.94
E C 0.92
R H 0.67
D H 0.73
F H 0.80
F H 0.79
K H 0.79
P H 0.75
T H 0.64
V C 0.55
Q C 0.74
D C 0.83
G C 0.79
N C 0.77
S C 0.48
V E 0.81
L E 0.87
R E 0.88
L E 0.83
L E 0.70
H E 0.56
Y C 0.64
P C 0.73
P C 0.80
I C 0.84
P C 0.85
K C 0.87
D C 0.81
A C 0.77
T C 0.73
G C 0.65
V C 0.54
R C 0.58
A C 0.59
G C 0.68
A C 0.69
H C 0.72
G C 0.74
D C 0.80
I C 0.73
N C 0.74
T E 0.40
I E 0.65
T E 0.75
L E 0.79
L E 0.78
L E 0.67
G C 0.51
A C 0.72
E C 0.76
E C 0.74
G C 0.70
G C 0.55
L E 0.72
E E 0.87
V E 0.89
L E 0.87
D C 0.54
R C 0.86
D C 0.93
G C 0.92
Q C 0.53
W E 0.89
L E 0.87
P E 0.87
I E 0.62
N C 0.50
P C 0.56
P C 0.79
P C 0.89
G C 0.92
C C 0.49
L E 0.86
V E 0.92
I E 0.87
N E 0.62
I C 0.48
G H 0.77
D H 0.90
M H 0.94
L H 0.95
E H 0.94
R H 0.92
L H 0.87
T H 0.66
N C 0.73
N C 0.89
V C 0.76
L C 0.58
P C 0.62
S C 0.61
T C 0.56
V C 0.47
H E 0.56
R E 0.71
V E 0.77
V E 0.72
N C 0.50
P C 0.73
P C 0.71
P C 0.62
E C 0.60
R C 0.69
R C 0.72
G C 0.76
V C 0.76
P C 0.69
R C 0.48
Y E 0.59
S E 0.68
T E 0.71
P E 0.66
F E 0.66
F E 0.64
L E 0.51
H C 0.67
F C 0.78
A C 0.81
S C 0.78
D C 0.79
Y C 0.51
E E 0.70
I E 0.70
K E 0.54
T C 0.66
L C 0.68
Q H 0.63
N H 0.66
C H 0.54
V C 0.70
T C 0.84
A C 0.76
E C 0.79
N C 0.82
P C 0.74
D C 0.68
R C 0.61
Y C 0.80
P C 0.84
E C 0.77
S C 0.59
I C 0.75
T H 0.87
A H 0.94
D H 0.95
E H 0.95
F H 0.95
L H 0.94
Q H 0.93
Q H 0.92
R H 0.88
L H 0.81
R H 0.63
E H 0.48
I C 0.64
K C 0.78
L C 0.86
A C 0.89
END