PFRMAT SS
TARGET T0427
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0427.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0427.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0427.t04.str2.rdb  (weight 1.54758)
METHOD T0427.t04.alpha.rdb  (weight 0.659012)
METHOD T0427.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0427.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0427.t2k.str2.rdb  (weight 1.54758)
METHOD T0427.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 T0427.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0427
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 T0427.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 2513
METHOD
METHOD ============================================
METHOD Comments from T0427.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0427
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 T0427.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 2513
METHOD
METHOD ============================================
METHOD Comments from T0427.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0427
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 T0427.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 2513
METHOD
METHOD ============================================
METHOD Comments from T0427.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0427
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 T0427.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 2513
METHOD
METHOD ============================================
METHOD Comments from T0427.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0427
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 T0427.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 856
METHOD
METHOD ============================================
METHOD Comments from T0427.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0427
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 T0427.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 856
METHOD
METHOD ============================================
METHOD Comments from T0427.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0427
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 T0427.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 856
METHOD
METHOD ============================================
METHOD Comments from T0427.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0427
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 T0427.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 856
METHOD
METHOD ============================================
MODEL 1
M C 0.85
S C 0.50
V E 0.76
Q E 0.82
L C 0.51
V C 0.80
K C 0.91
G C 0.81
V E 0.68
N E 0.91
L E 0.93
H E 0.92
V E 0.91
I E 0.85
P E 0.69
T C 0.75
E C 0.86
K C 0.89
Y C 0.82
K C 0.70
T E 0.77
V E 0.90
R E 0.92
L E 0.93
L E 0.93
V E 0.92
R E 0.91
F E 0.84
N E 0.61
T C 0.66
R C 0.84
L C 0.78
N C 0.70
H C 0.72
E C 0.77
T C 0.49
I H 0.58
T H 0.61
K H 0.80
R H 0.82
T H 0.82
L H 0.79
L H 0.80
S H 0.86
S H 0.88
L H 0.86
M H 0.78
E H 0.61
T C 0.58
N C 0.69
S C 0.63
L C 0.57
N C 0.50
Y H 0.54
P H 0.56
N H 0.84
Q H 0.93
V H 0.95
K H 0.95
L H 0.96
S H 0.95
E H 0.95
R H 0.93
L H 0.88
A H 0.75
E C 0.52
L C 0.74
Y C 0.78
G C 0.75
A C 0.77
S C 0.82
F C 0.85
G H 0.91
I H 0.94
G H 0.95
V H 0.96
S H 0.95
K H 0.95
K H 0.94
G H 0.93
N H 0.90
Q H 0.78
H H 0.49
W C 0.75
F C 0.56
N E 0.67
I E 0.73
S E 0.71
M E 0.61
N E 0.52
I C 0.49
V C 0.64
N C 0.72
D C 0.66
H C 0.46
Y E 0.72
L E 0.81
Q E 0.81
D E 0.77
S E 0.57
Q E 0.47
V C 0.52
L C 0.65
A H 0.66
E H 0.70
A H 0.68
V H 0.87
D H 0.93
F H 0.94
L H 0.95
K H 0.95
E H 0.93
I H 0.92
I H 0.90
F H 0.89
A H 0.90
P H 0.88
N H 0.86
I H 0.76
Q H 0.57
A C 0.77
G C 0.78
Q C 0.77
F C 0.86
E C 0.91
A H 0.90
E H 0.92
T H 0.94
F H 0.95
Q H 0.95
R H 0.95
E H 0.95
K H 0.95
E H 0.95
N H 0.96
L H 0.96
K H 0.96
A H 0.96
Y H 0.95
L H 0.95
E H 0.93
S H 0.87
I H 0.78
V H 0.62
E C 0.64
D C 0.86
K H 0.74
Q H 0.84
T H 0.91
Y H 0.93
A H 0.92
S H 0.93
L H 0.94
A H 0.94
L H 0.94
Q H 0.93
S H 0.90
V H 0.83
Y H 0.61
F C 0.73
N C 0.82
Q C 0.83
S C 0.86
E C 0.84
D C 0.77
Q C 0.75
K C 0.75
I C 0.75
P C 0.78
S C 0.74
F C 0.79
G C 0.86
T C 0.83
V H 0.86
A H 0.87
A H 0.84
L H 0.83
A H 0.68
E C 0.60
E C 0.79
T C 0.88
A H 0.93
A H 0.94
S H 0.95
L H 0.96
A H 0.96
A H 0.95
Y H 0.95
Y H 0.94
Q H 0.91
K H 0.84
M H 0.70
L C 0.60
A C 0.81
E C 0.78
D C 0.85
Q C 0.72
V E 0.74
D E 0.91
I E 0.93
F E 0.93
V E 0.92
L E 0.73
G C 0.61
D C 0.77
V C 0.76
N C 0.89
E H 0.89
A H 0.94
E H 0.95
L H 0.95
V H 0.96
P H 0.96
L H 0.96
F H 0.95
K H 0.95
Q H 0.92
L H 0.86
P H 0.68
F C 0.60
T C 0.67
P C 0.77
R C 0.79
E C 0.73
E C 0.76
G C 0.77
K C 0.78
A C 0.79
A C 0.80
I C 0.80
F C 0.79
Y C 0.80
N C 0.80
Q C 0.80
P C 0.82
I C 0.80
R C 0.76
N C 0.76
V C 0.75
I C 0.68
E E 0.50
E E 0.76
R E 0.84
T E 0.83
E E 0.73
R C 0.51
E C 0.76
V C 0.81
L C 0.68
A C 0.59
Q C 0.46
S E 0.42
K E 0.65
L E 0.80
N E 0.80
L E 0.77
A E 0.65
Y E 0.46
N C 0.60
T C 0.75
D C 0.80
I C 0.82
Y C 0.80
Y C 0.78
G C 0.84
D C 0.81
S H 0.53
Y H 0.56
Y H 0.77
F H 0.86
A H 0.94
L H 0.95
Q H 0.96
V H 0.96
F H 0.96
N H 0.95
G H 0.92
I H 0.87
F H 0.59
G C 0.76
G C 0.83
F C 0.75
P C 0.50
H H 0.61
S H 0.82
K H 0.93
L H 0.93
F H 0.94
M H 0.94
N H 0.94
V H 0.94
R H 0.93
E H 0.90
K H 0.81
E C 0.53
H C 0.84
L C 0.65
A E 0.55
Y E 0.65
Y E 0.72
A E 0.69
S E 0.68
S E 0.59
S E 0.52
I E 0.45
D C 0.57
T C 0.69
F C 0.74
R C 0.76
G C 0.66
F E 0.65
M E 0.86
T E 0.91
V E 0.91
Q E 0.87
T E 0.76
G E 0.52
I C 0.72
D C 0.86
G C 0.52
K C 0.50
N H 0.57
R H 0.91
N H 0.95
Q H 0.95
V H 0.96
L H 0.96
R H 0.96
L H 0.96
I H 0.96
S H 0.96
T H 0.96
E H 0.96
L H 0.96
E H 0.96
N H 0.95
I H 0.94
R H 0.92
L H 0.69
G C 0.72
K C 0.92
I C 0.92
R C 0.94
E H 0.93
L H 0.94
E H 0.95
I H 0.96
E H 0.96
Q H 0.96
T H 0.96
K H 0.96
A H 0.95
M H 0.95
L H 0.94
K H 0.92
N H 0.85
Q H 0.76
Y H 0.75
I H 0.72
L H 0.66
A H 0.52
L C 0.54
D C 0.68
N C 0.79
A H 0.80
G H 0.89
A H 0.93
W H 0.95
L H 0.95
E H 0.95
K H 0.95
E H 0.95
Y H 0.94
L H 0.94
N H 0.93
E H 0.92
L H 0.85
M H 0.64
P C 0.73
Q C 0.88
T C 0.85
M C 0.72
L C 0.72
T C 0.71
A H 0.91
E H 0.93
E H 0.93
W H 0.94
I H 0.95
A H 0.94
R H 0.92
I H 0.86
N H 0.74
A C 0.52
V C 0.78
T C 0.90
I H 0.93
P H 0.94
E H 0.95
I H 0.96
Q H 0.96
E H 0.96
V H 0.95
A H 0.94
K H 0.92
R H 0.87
L H 0.79
E C 0.49
L C 0.74
Q C 0.79
A C 0.83
I C 0.78
F E 0.74
F E 0.91
L E 0.93
E E 0.92
G E 0.89
E E 0.64
T C 0.70
E C 0.83
N C 0.86
D C 0.92
END