PFRMAT SS
TARGET T0398
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0398.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0398.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0398.t04.str2.rdb  (weight 1.54758)
METHOD T0398.t04.alpha.rdb  (weight 0.659012)
METHOD T0398.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0398.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0398.t2k.str2.rdb  (weight 1.54758)
METHOD T0398.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 T0398.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0398
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 T0398.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 1138.46
METHOD
METHOD ============================================
METHOD Comments from T0398.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0398
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 T0398.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 1138.46
METHOD
METHOD ============================================
METHOD Comments from T0398.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0398
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 T0398.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 1138.46
METHOD
METHOD ============================================
METHOD Comments from T0398.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0398
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 T0398.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 1138.46
METHOD
METHOD ============================================
METHOD Comments from T0398.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0398
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 T0398.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 1610
METHOD
METHOD ============================================
METHOD Comments from T0398.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0398
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 T0398.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 1610
METHOD
METHOD ============================================
METHOD Comments from T0398.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0398
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 T0398.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 1610
METHOD
METHOD ============================================
METHOD Comments from T0398.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0398
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 T0398.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 1610
METHOD
METHOD ============================================
MODEL 1
M C 0.85
L C 0.80
T C 0.74
G C 0.54
K E 0.71
H E 0.84
V E 0.87
V E 0.88
I E 0.82
I C 0.52
G C 0.80
G C 0.72
D C 0.57
A H 0.83
R H 0.90
Q H 0.93
L H 0.94
E H 0.94
I H 0.94
I H 0.89
R H 0.77
K H 0.79
L H 0.74
S H 0.69
T H 0.59
F H 0.52
D C 0.43
A C 0.50
K C 0.49
I E 0.50
S E 0.53
L E 0.48
V C 0.53
G C 0.71
F C 0.79
D C 0.80
Q C 0.81
L H 0.75
D H 0.89
D H 0.89
G H 0.90
F H 0.90
I H 0.88
G H 0.86
V H 0.79
T H 0.75
K H 0.70
M H 0.59
R H 0.55
I H 0.48
D H 0.67
E H 0.75
V H 0.76
D H 0.73
W H 0.61
N H 0.48
T C 0.58
V C 0.68
D C 0.68
A E 0.46
I E 0.65
L E 0.74
L E 0.72
P E 0.54
I C 0.65
S C 0.74
G C 0.79
T C 0.81
N C 0.62
E C 0.53
A C 0.50
G H 0.46
K H 0.45
V H 0.43
D E 0.42
T E 0.37
I H 0.39
F C 0.50
S C 0.50
N C 0.43
E C 0.45
S C 0.50
I C 0.57
V C 0.51
L C 0.50
T C 0.61
E H 0.80
E H 0.80
M H 0.79
I H 0.73
E H 0.61
K H 0.51
T C 0.55
P C 0.64
N C 0.61
H C 0.53
C E 0.51
V E 0.65
V E 0.78
Y E 0.80
S E 0.76
G E 0.61
I C 0.47
S C 0.60
N C 0.56
T C 0.48
Y H 0.47
L H 0.48
N H 0.56
Q H 0.63
C H 0.69
M H 0.72
K H 0.78
K H 0.78
T H 0.86
N H 0.86
R H 0.84
T H 0.80
L H 0.83
V H 0.82
K H 0.80
L H 0.76
M H 0.66
E H 0.62
R H 0.68
D H 0.67
D H 0.75
I H 0.84
A H 0.85
I H 0.87
Y H 0.86
N H 0.83
S H 0.82
I H 0.82
P H 0.82
T H 0.78
A H 0.74
E H 0.73
G H 0.72
T H 0.72
I H 0.65
M H 0.59
M H 0.51
A H 0.48
I C 0.48
Q C 0.56
H C 0.60
T C 0.66
D C 0.69
F C 0.49
T E 0.50
I C 0.60
H C 0.84
G C 0.90
A C 0.72
N E 0.77
V E 0.92
A E 0.93
V E 0.93
L E 0.85
G C 0.52
L C 0.80
G C 0.67
R H 0.92
V H 0.94
G H 0.95
M H 0.96
S H 0.96
V H 0.96
A H 0.96
R H 0.96
K H 0.96
F H 0.96
A H 0.93
A H 0.84
L C 0.66
G C 0.94
A C 0.90
K E 0.57
V E 0.91
K E 0.93
V E 0.93
G E 0.84
A C 0.52
R C 0.89
E C 0.88
S H 0.53
D H 0.64
L H 0.78
L H 0.86
A H 0.87
R H 0.90
I H 0.91
A H 0.91
E H 0.86
M H 0.50
G C 0.84
M C 0.84
E C 0.66
P C 0.45
F C 0.45
H C 0.50
I C 0.50
S C 0.48
K H 0.53
A H 0.54
A H 0.49
Q C 0.50
E C 0.47
L E 0.53
R E 0.69
D E 0.81
V E 0.84
D E 0.82
V E 0.69
C C 0.52
I C 0.74
N C 0.85
T C 0.84
I C 0.82
P C 0.79
A C 0.62
L C 0.60
V C 0.54
V C 0.58
T C 0.80
A H 0.93
N H 0.94
V H 0.94
L H 0.94
A H 0.85
E H 0.58
M C 0.76
P C 0.89
S C 0.86
H C 0.88
T E 0.69
F E 0.92
V E 0.93
I E 0.92
D E 0.86
L E 0.55
A C 0.63
S C 0.76
K C 0.81
P C 0.77
G C 0.70
G C 0.65
T C 0.64
D H 0.67
F H 0.92
R H 0.94
Y H 0.95
A H 0.94
E H 0.92
K H 0.88
R H 0.59
G C 0.80
I C 0.78
K C 0.69
A E 0.57
L E 0.71
L E 0.64
V C 0.48
P C 0.71
G C 0.77
L C 0.75
P C 0.67
G C 0.50
I E 0.46
V C 0.56
A C 0.74
P C 0.84
K C 0.82
T C 0.75
A C 0.60
G H 0.60
R H 0.83
I H 0.86
L H 0.85
A H 0.78
D H 0.63
V H 0.51
L C 0.51
V C 0.46
K H 0.47
L H 0.47
L H 0.36
A C 0.45
E C 0.67
P C 0.82
S C 0.91
END