PFRMAT SS
TARGET T0506
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0506.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0506.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0506.t04.str2.rdb  (weight 1.54758)
METHOD T0506.t04.alpha.rdb  (weight 0.659012)
METHOD T0506.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0506.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0506.t2k.str2.rdb  (weight 1.54758)
METHOD T0506.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 T0506.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0506
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 T0506.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 1355
METHOD
METHOD ============================================
METHOD Comments from T0506.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0506
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 T0506.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 1355
METHOD
METHOD ============================================
METHOD Comments from T0506.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0506
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 T0506.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 1355
METHOD
METHOD ============================================
METHOD Comments from T0506.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0506
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 T0506.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 1355
METHOD
METHOD ============================================
METHOD Comments from T0506.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0506
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 T0506.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 157
METHOD
METHOD ============================================
METHOD Comments from T0506.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0506
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 T0506.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 157
METHOD
METHOD ============================================
METHOD Comments from T0506.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0506
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 T0506.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 157
METHOD
METHOD ============================================
METHOD Comments from T0506.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0506
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 T0506.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 157
METHOD
METHOD ============================================
MODEL 1
M C 0.80
L C 0.71
D C 0.75
V C 0.80
A C 0.74
P C 0.76
P C 0.74
V C 0.80
I C 0.77
T C 0.75
P C 0.75
R C 0.75
G C 0.72
T C 0.68
K C 0.70
I C 0.71
E C 0.74
P C 0.73
S C 0.71
A C 0.78
G C 0.82
A C 0.85
P C 0.85
F H 0.50
E H 0.62
A H 0.86
V H 0.93
R H 0.94
V H 0.96
A H 0.96
R H 0.96
D H 0.96
V H 0.95
L H 0.94
H H 0.87
T H 0.76
S H 0.62
R C 0.53
T H 0.51
A H 0.50
A H 0.40
L E 0.45
A E 0.43
T C 0.41
L C 0.58
D C 0.68
P C 0.71
V C 0.73
S C 0.83
G C 0.88
Y C 0.81
P C 0.66
Y C 0.56
T E 0.50
T E 0.64
A E 0.77
T E 0.79
N E 0.76
I E 0.70
G E 0.62
I E 0.61
E C 0.84
P C 0.86
D C 0.93
G C 0.92
T C 0.82
P E 0.69
F E 0.85
F E 0.89
F E 0.86
A E 0.64
A C 0.61
G H 0.50
L H 0.62
T H 0.75
L H 0.81
H H 0.78
A H 0.87
R H 0.88
N H 0.85
M H 0.80
E H 0.58
T C 0.57
D C 0.87
A C 0.85
R C 0.71
I E 0.63
S E 0.83
V E 0.91
T E 0.90
L E 0.83
A E 0.63
P C 0.64
F C 0.81
G C 0.85
K C 0.86
G C 0.87
D C 0.85
A C 0.67
L C 0.64
T C 0.66
L C 0.76
P C 0.66
R E 0.72
L E 0.88
T E 0.90
L E 0.92
V E 0.87
G E 0.84
R E 0.87
A E 0.83
D E 0.79
R E 0.68
I C 0.80
G C 0.90
P C 0.56
D H 0.50
E H 0.57
V H 0.70
P H 0.87
L H 0.93
A H 0.94
I H 0.95
A H 0.95
R H 0.95
Y H 0.95
I H 0.94
A H 0.89
R H 0.76
Y C 0.73
P C 0.61
K C 0.57
A H 0.55
K H 0.58
L H 0.52
Y C 0.44
L C 0.64
S C 0.71
L C 0.74
P C 0.81
D C 0.77
T E 0.55
R E 0.76
L E 0.90
Y E 0.90
R E 0.92
L E 0.89
R E 0.84
T E 0.79
E E 0.73
G E 0.86
V E 0.88
Q E 0.90
I E 0.89
N E 0.73
G C 0.54
G C 0.75
P C 0.71
A C 0.67
R C 0.53
N E 0.55
A E 0.64
S E 0.75
N E 0.55
I C 0.73
T H 0.80
P H 0.83
A H 0.86
D H 0.82
L H 0.70
R H 0.53
T C 0.66
D C 0.81
L C 0.60
S C 0.58
G C 0.56
A H 0.60
E H 0.61
E H 0.77
L H 0.83
M H 0.84
A H 0.85
A H 0.83
A H 0.88
E H 0.91
S H 0.93
E H 0.94
A H 0.93
T H 0.91
R H 0.80
L H 0.66
N C 0.54
A H 0.62
I H 0.53
K H 0.66
G H 0.90
E H 0.94
A H 0.95
S H 0.96
R H 0.96
L H 0.96
A H 0.95
V H 0.93
L H 0.87
A H 0.74
G H 0.48
A C 0.71
K C 0.83
T C 0.79
G C 0.80
R C 0.60
W E 0.69
K E 0.83
I E 0.87
T E 0.83
S E 0.79
I E 0.74
D C 0.70
P C 0.77
D C 0.87
G C 0.73
I C 0.56
D E 0.78
L E 0.85
A E 0.82
S E 0.60
A C 0.75
S C 0.82
D C 0.67
L E 0.51
A E 0.65
R E 0.74
L E 0.71
W E 0.65
F E 0.52
A C 0.56
E C 0.72
R C 0.79
V C 0.82
E C 0.84
T C 0.87
L H 0.75
K H 0.88
Q H 0.91
F H 0.93
E H 0.95
K H 0.95
A H 0.95
L H 0.95
A H 0.94
Q H 0.90
L H 0.76
L H 0.50
K C 0.82
END