PFRMAT SS
TARGET T0393
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0393.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0393.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0393.t04.str2.rdb  (weight 1.54758)
METHOD T0393.t04.alpha.rdb  (weight 0.659012)
METHOD T0393.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0393.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0393.t2k.str2.rdb  (weight 1.54758)
METHOD T0393.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 T0393.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 2001
METHOD
METHOD ============================================
METHOD Comments from T0393.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 2001
METHOD
METHOD ============================================
METHOD Comments from T0393.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 2001
METHOD
METHOD ============================================
METHOD Comments from T0393.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 2001
METHOD
METHOD ============================================
METHOD Comments from T0393.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 667
METHOD
METHOD ============================================
METHOD Comments from T0393.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 667
METHOD
METHOD ============================================
METHOD Comments from T0393.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 667
METHOD
METHOD ============================================
METHOD Comments from T0393.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0393
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 T0393.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 667
METHOD
METHOD ============================================
MODEL 1
M C 0.83
K C 0.74
R C 0.76
S C 0.78
I C 0.61
E C 0.67
D C 0.79
T C 0.84
P C 0.58
I E 0.91
V E 0.93
L E 0.93
I E 0.86
G C 0.50
A C 0.79
G C 0.61
N H 0.91
L H 0.93
A H 0.95
T H 0.96
N H 0.96
L H 0.96
A H 0.96
K H 0.96
A H 0.96
L H 0.96
Y H 0.94
R H 0.88
K C 0.67
G C 0.94
F C 0.90
R C 0.51
I E 0.90
V E 0.92
Q E 0.92
V E 0.90
Y E 0.73
S C 0.67
R C 0.88
T C 0.91
E H 0.87
E H 0.91
S H 0.93
A H 0.95
R H 0.95
E H 0.95
L H 0.94
A H 0.94
Q H 0.90
K H 0.83
V C 0.49
E C 0.89
A C 0.84
E C 0.68
Y C 0.53
T C 0.64
T C 0.75
D C 0.79
L H 0.81
A H 0.88
E H 0.89
V H 0.88
N H 0.78
P H 0.55
Y C 0.73
A C 0.88
K C 0.87
L E 0.91
Y E 0.93
I E 0.93
V E 0.91
S E 0.63
L C 0.78
K C 0.87
D C 0.68
S C 0.53
A H 0.63
F H 0.82
A H 0.90
E H 0.91
L H 0.92
L H 0.92
Q H 0.89
G H 0.83
I H 0.78
V H 0.76
E H 0.73
G H 0.64
K C 0.50
R C 0.70
E C 0.83
E C 0.92
A C 0.73
L E 0.83
M E 0.91
V E 0.91
H E 0.88
T E 0.60
A C 0.66
G C 0.74
S C 0.75
I C 0.77
P C 0.75
M H 0.62
N H 0.66
V H 0.71
W H 0.75
E H 0.79
G H 0.80
H H 0.78
V H 0.70
P H 0.56
H C 0.60
Y C 0.82
G C 0.79
V E 0.48
F E 0.73
Y E 0.74
P E 0.67
M C 0.48
Q C 0.71
T C 0.75
F C 0.75
S C 0.77
K C 0.61
Q H 0.51
R H 0.64
E H 0.69
V H 0.65
D H 0.56
F C 0.54
K C 0.63
E C 0.66
I C 0.57
P C 0.43
F E 0.63
F E 0.62
I E 0.47
E C 0.59
A C 0.78
S C 0.87
S C 0.88
T H 0.91
E H 0.93
D H 0.94
A H 0.95
A H 0.95
F H 0.94
L H 0.94
K H 0.95
A H 0.95
I H 0.95
A H 0.94
S H 0.91
T H 0.81
L H 0.50
S C 0.85
N C 0.82
R C 0.59
V E 0.70
Y E 0.82
D E 0.83
A E 0.54
D C 0.80
S C 0.60
E C 0.55
Q H 0.59
R H 0.65
K H 0.71
S H 0.74
L H 0.75
H H 0.77
L H 0.81
A H 0.85
A H 0.85
V H 0.80
F H 0.73
T H 0.83
C H 0.92
N H 0.94
F H 0.95
T H 0.96
N H 0.96
H H 0.96
M H 0.96
Y H 0.96
A H 0.96
L H 0.96
A H 0.96
A H 0.96
E H 0.95
L H 0.95
L H 0.95
K H 0.94
K H 0.85
Y C 0.60
N C 0.93
L C 0.93
P C 0.92
F H 0.84
D H 0.88
V H 0.90
M H 0.91
L H 0.94
P H 0.94
L H 0.95
I H 0.95
D H 0.94
E H 0.93
T H 0.92
A H 0.90
R H 0.86
K H 0.75
V H 0.79
H H 0.82
E H 0.77
L H 0.64
E C 0.55
P C 0.53
K C 0.49
T C 0.54
A C 0.62
Q C 0.69
T C 0.76
G C 0.66
P C 0.52
A H 0.50
I H 0.54
R H 0.51
Y C 0.66
D C 0.61
E H 0.89
N H 0.94
V H 0.95
I H 0.96
G H 0.96
N H 0.96
H H 0.96
L H 0.95
R H 0.94
M H 0.90
L H 0.79
A H 0.63
D C 0.52
D C 0.64
P C 0.67
A H 0.72
M H 0.80
Q H 0.85
R H 0.88
L H 0.90
Y H 0.90
E H 0.89
L H 0.89
L H 0.84
S H 0.67
R H 0.55
S C 0.50
I C 0.58
H C 0.69
E C 0.68
R C 0.74
Q C 0.89
END