PFRMAT SS
TARGET T0582
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0582.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0582.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0582.t04.str2.rdb  (weight 1.54758)
METHOD T0582.t04.alpha.rdb  (weight 0.659012)
METHOD T0582.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0582.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0582.t2k.str2.rdb  (weight 1.54758)
METHOD T0582.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 T0582.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0582
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 T0582.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 1665
METHOD
METHOD ============================================
METHOD Comments from T0582.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0582
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 T0582.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 1665
METHOD
METHOD ============================================
METHOD Comments from T0582.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0582
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 T0582.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 1665
METHOD
METHOD ============================================
METHOD Comments from T0582.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0582
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 T0582.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 1665
METHOD
METHOD ============================================
METHOD Comments from T0582.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0582
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 T0582.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 396
METHOD
METHOD ============================================
METHOD Comments from T0582.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0582
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 T0582.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 396
METHOD
METHOD ============================================
METHOD Comments from T0582.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0582
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 T0582.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 396
METHOD
METHOD ============================================
METHOD Comments from T0582.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0582
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 T0582.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 396
METHOD
METHOD ============================================
MODEL 1
M C 0.86
E C 0.72
I C 0.67
N C 0.77
A C 0.73
D C 0.77
F C 0.70
T C 0.71
K C 0.66
P C 0.55
V E 0.69
V E 0.81
I E 0.74
D C 0.50
T C 0.50
D C 0.58
Q H 0.48
L C 0.68
E C 0.68
W C 0.48
R E 0.51
P E 0.51
S C 0.67
P C 0.81
M C 0.85
K C 0.82
G C 0.74
V C 0.46
E E 0.68
R E 0.64
R E 0.60
M E 0.55
L E 0.41
D C 0.42
R C 0.58
I C 0.72
G C 0.82
G C 0.79
E C 0.71
V C 0.67
A C 0.62
R E 0.57
A E 0.81
T E 0.88
S E 0.91
I E 0.92
V E 0.91
R E 0.90
Y E 0.75
A C 0.71
P C 0.90
G C 0.92
S C 0.81
R C 0.67
F C 0.66
S C 0.73
A C 0.65
H C 0.62
T C 0.63
H C 0.80
D C 0.86
G C 0.87
G C 0.75
E E 0.58
E E 0.86
F E 0.91
I E 0.93
V E 0.92
L E 0.90
D E 0.81
G E 0.71
V E 0.77
F E 0.73
Q E 0.62
D C 0.58
E C 0.78
H C 0.84
G C 0.84
D C 0.73
Y C 0.59
P C 0.80
A C 0.76
G C 0.75
T C 0.50
Y E 0.77
V E 0.81
R E 0.77
N C 0.52
P C 0.86
P C 0.89
T C 0.90
T C 0.81
S C 0.72
H C 0.63
V C 0.65
P C 0.57
G C 0.54
S C 0.68
A C 0.83
E C 0.87
G C 0.88
C C 0.59
T E 0.77
I E 0.87
F E 0.91
V E 0.90
K E 0.88
L E 0.83
W E 0.76
Q E 0.58
F C 0.67
D C 0.86
P C 0.65
A C 0.62
D C 0.57
R C 0.63
T C 0.60
Q C 0.53
F E 0.48
S E 0.56
K E 0.49
N C 0.51
M C 0.57
E C 0.67
A C 0.74
E C 0.58
L C 0.56
G C 0.57
A C 0.68
P C 0.73
V C 0.76
E C 0.80
G C 0.73
I E 0.51
S E 0.74
T E 0.77
S E 0.72
L E 0.66
L E 0.46
H C 0.54
E C 0.72
D C 0.84
E C 0.83
R C 0.78
E C 0.49
T E 0.79
V E 0.88
T E 0.90
H E 0.91
R E 0.88
K E 0.85
L E 0.61
E C 0.77
P C 0.88
G C 0.90
A C 0.66
N E 0.63
L E 0.63
T E 0.53
S C 0.49
E C 0.57
A C 0.74
A C 0.79
G C 0.83
G C 0.66
I E 0.68
E E 0.89
V E 0.91
L E 0.93
V E 0.93
L E 0.91
D E 0.84
G E 0.79
D E 0.86
V E 0.85
T E 0.76
V E 0.51
N C 0.83
D C 0.87
E C 0.60
V E 0.60
L E 0.55
G C 0.79
R C 0.84
N C 0.85
A C 0.60
W E 0.72
L E 0.76
R E 0.72
L C 0.56
P C 0.82
E C 0.87
G C 0.88
E C 0.84
A C 0.68
L C 0.59
S C 0.52
A E 0.59
T E 0.61
A E 0.63
G C 0.63
A C 0.82
R C 0.85
G C 0.81
A C 0.49
K E 0.87
I E 0.91
W E 0.91
M E 0.88
K E 0.73
T C 0.49
G C 0.72
H C 0.71
L C 0.65
R C 0.66
F C 0.66
V C 0.79
R C 0.84
T C 0.85
P C 0.76
E C 0.76
V C 0.90
END