PFRMAT SS
TARGET T0438
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0438.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0438.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0438.t04.str2.rdb  (weight 1.54758)
METHOD T0438.t04.alpha.rdb  (weight 0.659012)
METHOD T0438.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0438.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0438.t2k.str2.rdb  (weight 1.54758)
METHOD T0438.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 T0438.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0438
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 T0438.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 1045.57
METHOD
METHOD ============================================
METHOD Comments from T0438.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0438
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 T0438.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 1045.57
METHOD
METHOD ============================================
METHOD Comments from T0438.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0438
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 T0438.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 1045.57
METHOD
METHOD ============================================
METHOD Comments from T0438.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0438
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 T0438.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 1045.57
METHOD
METHOD ============================================
METHOD Comments from T0438.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0438
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 T0438.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 576
METHOD
METHOD ============================================
METHOD Comments from T0438.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0438
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 T0438.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 576
METHOD
METHOD ============================================
METHOD Comments from T0438.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0438
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 T0438.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 576
METHOD
METHOD ============================================
METHOD Comments from T0438.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0438
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 T0438.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 576
METHOD
METHOD ============================================
MODEL 1
M C 0.72
Q H 0.49
W H 0.51
Q C 0.48
E H 0.56
L H 0.78
Y H 0.82
R H 0.83
Q H 0.78
R H 0.64
V H 0.51
C C 0.62
S C 0.71
A C 0.84
D H 0.94
E H 0.95
A H 0.95
V H 0.95
V H 0.91
D H 0.78
S H 0.65
L C 0.64
K C 0.84
P C 0.88
G C 0.91
T C 0.60
K E 0.84
V E 0.89
V E 0.87
F E 0.75
G C 0.48
H C 0.66
A C 0.70
A C 0.75
A C 0.80
A C 0.76
P C 0.49
V H 0.72
R H 0.77
F H 0.83
S H 0.91
Q H 0.94
A H 0.95
M H 0.95
Y H 0.95
R H 0.93
Q H 0.91
R H 0.89
E H 0.84
K H 0.73
L C 0.49
E C 0.67
N C 0.65
I C 0.61
T C 0.53
V E 0.48
F E 0.62
H E 0.62
M E 0.55
L E 0.40
Y C 0.54
F C 0.72
G C 0.78
D C 0.54
A H 0.52
P H 0.59
H H 0.55
L H 0.49
A C 0.52
P H 0.51
E H 0.48
M C 0.53
R C 0.66
S C 0.62
H C 0.45
V E 0.62
H E 0.68
P E 0.64
T C 0.50
L C 0.55
N C 0.61
F C 0.64
L C 0.76
E C 0.80
G H 0.75
N H 0.84
S H 0.90
R H 0.91
P H 0.90
A H 0.87
S H 0.82
R H 0.73
D C 0.51
R C 0.73
R C 0.66
V C 0.62
D C 0.65
F C 0.58
I C 0.62
P C 0.56
C C 0.47
H C 0.46
F C 0.43
H C 0.47
E C 0.49
V H 0.51
P H 0.85
E H 0.90
L H 0.92
F H 0.91
R H 0.89
Q H 0.59
G C 0.79
F C 0.88
F C 0.86
P C 0.87
L C 0.82
D C 0.67
V E 0.92
A E 0.93
V E 0.93
V E 0.90
Q E 0.69
V C 0.61
S C 0.78
T C 0.81
P C 0.71
N C 0.83
E C 0.83
E C 0.88
G C 0.84
Y C 0.65
C E 0.71
S E 0.62
F E 0.48
G C 0.61
V C 0.64
S C 0.70
C C 0.67
D C 0.74
Y C 0.66
T C 0.63
K H 0.93
A H 0.94
A H 0.94
A H 0.93
E H 0.84
C H 0.50
A C 0.82
P C 0.84
V E 0.71
V E 0.91
V E 0.92
A E 0.92
E E 0.85
V E 0.54
N C 0.80
K C 0.85
Q C 0.87
M C 0.84
P C 0.80
F C 0.69
I C 0.69
G C 0.77
G C 0.81
E C 0.78
N C 0.77
L C 0.75
I C 0.74
H C 0.84
I H 0.71
S H 0.67
K H 0.58
L E 0.52
T E 0.72
H E 0.90
I E 0.92
I E 0.91
E E 0.78
V C 0.66
D C 0.86
E C 0.87
P C 0.82
I C 0.78
A C 0.73
E C 0.75
V C 0.82
L C 0.82
P C 0.81
P C 0.87
A C 0.90
G C 0.88
S C 0.89
D H 0.91
L H 0.94
E H 0.95
L H 0.96
R H 0.96
I H 0.95
G H 0.96
Q H 0.96
N H 0.95
C H 0.94
A H 0.93
S H 0.85
L H 0.75
I C 0.56
K C 0.76
D C 0.88
G C 0.87
D C 0.65
T E 0.58
L E 0.71
Q E 0.73
L E 0.55
G C 0.50
I C 0.59
G C 0.66
G C 0.59
I H 0.65
P H 0.84
D H 0.91
A H 0.93
V H 0.92
L H 0.88
R H 0.79
A H 0.64
L C 0.71
E C 0.79
G C 0.77
H C 0.76
K C 0.69
D E 0.53
L E 0.80
G E 0.86
I E 0.86
H E 0.79
T E 0.56
E C 0.43
M C 0.44
F H 0.39
T H 0.52
D H 0.59
G H 0.66
V H 0.72
M H 0.74
R H 0.73
M H 0.74
I H 0.72
R H 0.69
K C 0.60
G C 0.87
I C 0.71
I C 0.50
N C 0.71
G C 0.48
K H 0.48
K H 0.49
K C 0.39
T C 0.45
L C 0.56
H C 0.70
P C 0.76
E C 0.70
K E 0.50
V E 0.78
V E 0.83
T E 0.81
S E 0.65
L C 0.53
I C 0.63
F C 0.67
G C 0.70
S C 0.62
K H 0.91
E H 0.93
L H 0.94
Y H 0.94
D H 0.93
F H 0.90
V H 0.85
N H 0.66
N C 0.57
N C 0.83
P C 0.67
V C 0.58
I C 0.47
E C 0.45
C C 0.54
Y C 0.72
P C 0.76
V C 0.61
D C 0.57
Y C 0.56
I C 0.67
N C 0.78
N C 0.82
P H 0.83
D H 0.89
V H 0.90
I H 0.89
G H 0.79
K H 0.52
N C 0.76
D C 0.76
R C 0.65
M E 0.42
V E 0.77
S E 0.84
I E 0.81
N E 0.61
S E 0.57
C E 0.61
L E 0.74
E E 0.76
M E 0.72
D E 0.50
L H 0.41
M C 0.60
G C 0.61
Q C 0.46
A E 0.50
A E 0.42
S C 0.43
E C 0.51
S C 0.63
I C 0.71
G C 0.83
Y C 0.77
E C 0.49
Q E 0.65
F E 0.56
S C 0.64
G C 0.80
S C 0.67
G C 0.66
G C 0.55
Q H 0.68
V H 0.80
D H 0.82
F H 0.79
L H 0.73
R H 0.49
G C 0.63
A C 0.60
K C 0.46
R C 0.51
S C 0.81
K C 0.86
G C 0.92
G C 0.81
I E 0.50
S E 0.86
I E 0.91
M E 0.90
A E 0.85
F E 0.69
P E 0.53
S C 0.49
T C 0.51
A C 0.72
K C 0.82
K C 0.91
G C 0.90
T C 0.80
E C 0.65
S C 0.64
R C 0.54
I C 0.60
V C 0.70
P C 0.57
I C 0.43
L C 0.53
K C 0.64
E C 0.71
G C 0.69
A C 0.72
C C 0.71
V C 0.66
T C 0.67
T C 0.76
G C 0.76
R C 0.64
N C 0.62
E C 0.49
V E 0.52
D E 0.60
Y E 0.86
V E 0.90
V E 0.87
T E 0.71
E C 0.51
Y C 0.55
G C 0.45
V E 0.54
A E 0.58
R E 0.59
L C 0.53
R C 0.81
G C 0.90
A C 0.89
T C 0.90
L H 0.91
R H 0.94
Q H 0.95
R H 0.96
A H 0.96
E H 0.95
A H 0.95
L H 0.95
T H 0.93
A H 0.87
I H 0.69
A C 0.70
H C 0.85
P H 0.74
D H 0.76
F H 0.78
R H 0.93
P H 0.95
A H 0.95
L H 0.95
E H 0.96
E H 0.95
E H 0.95
I H 0.93
R H 0.90
R H 0.85
R H 0.58
F C 0.67
E C 0.70
L C 0.72
E C 0.78
H C 0.76
H C 0.78
H C 0.72
H C 0.68
H C 0.81
H C 0.92
END