PFRMAT SS
TARGET T0611
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0611.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0611.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0611.t04.str2.rdb  (weight 1.54758)
METHOD T0611.t04.alpha.rdb  (weight 0.659012)
METHOD T0611.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0611.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0611.t2k.str2.rdb  (weight 1.54758)
METHOD T0611.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 T0611.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0611
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 T0611.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 1880
METHOD
METHOD ============================================
METHOD Comments from T0611.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0611
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 T0611.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 1880
METHOD
METHOD ============================================
METHOD Comments from T0611.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0611
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 T0611.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 1880
METHOD
METHOD ============================================
METHOD Comments from T0611.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0611
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 T0611.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 1880
METHOD
METHOD ============================================
METHOD Comments from T0611.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0611
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 T0611.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 6598
METHOD
METHOD ============================================
METHOD Comments from T0611.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0611
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 T0611.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 6598
METHOD
METHOD ============================================
METHOD Comments from T0611.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0611
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 T0611.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 6598
METHOD
METHOD ============================================
METHOD Comments from T0611.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0611
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 T0611.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 6598
METHOD
METHOD ============================================
MODEL 1
M C 0.87
T C 0.64
M H 0.71
K H 0.76
T H 0.81
R H 0.95
D H 0.96
K H 0.96
I H 0.96
L H 0.96
L H 0.96
S H 0.96
S H 0.96
L H 0.96
E H 0.96
L H 0.96
F H 0.95
N H 0.94
D H 0.82
K C 0.48
G C 0.85
E C 0.80
R C 0.67
N C 0.62
I C 0.57
T C 0.69
T H 0.94
N H 0.96
H H 0.96
I H 0.96
A H 0.96
A H 0.94
H H 0.88
L C 0.52
A C 0.92
I C 0.90
S C 0.88
P H 0.55
G H 0.63
N H 0.65
L H 0.64
Y H 0.53
Y H 0.46
H C 0.47
F C 0.75
R C 0.87
N C 0.89
K H 0.87
S H 0.93
D H 0.95
I H 0.96
I H 0.96
Y H 0.96
E H 0.96
I H 0.96
F H 0.95
Q H 0.94
E H 0.92
Y H 0.91
E H 0.91
K H 0.91
L H 0.91
V H 0.92
D H 0.92
Y H 0.91
Y H 0.89
L H 0.82
D H 0.74
I H 0.60
P C 0.61
E C 0.67
D C 0.75
R C 0.82
P C 0.85
I C 0.86
T H 0.85
L H 0.93
E H 0.95
D H 0.95
M H 0.96
T H 0.96
F H 0.96
Y H 0.96
L H 0.96
E H 0.96
S H 0.96
V H 0.95
F H 0.95
D H 0.93
G H 0.89
L H 0.84
W H 0.74
S H 0.58
Y C 0.60
R H 0.73
F H 0.81
F H 0.88
H H 0.91
R H 0.92
D H 0.92
L H 0.92
E H 0.90
Y H 0.84
L H 0.73
L H 0.53
D C 0.60
S C 0.71
D C 0.73
P H 0.79
R H 0.83
L H 0.88
R H 0.91
Q H 0.92
D H 0.93
Y H 0.93
R H 0.93
E H 0.93
F H 0.92
T H 0.92
N H 0.93
R H 0.93
C H 0.94
L H 0.95
A H 0.95
A H 0.95
I H 0.96
N H 0.96
R H 0.96
I H 0.96
F H 0.96
A H 0.95
K H 0.92
L H 0.89
A H 0.86
D H 0.81
A C 0.55
G C 0.89
I C 0.85
I C 0.76
Q C 0.87
P C 0.82
Q C 0.86
P C 0.86
E H 0.89
D H 0.94
L H 0.95
R H 0.96
S H 0.96
A H 0.96
M H 0.96
S H 0.96
L H 0.96
N H 0.96
V H 0.96
W H 0.95
L H 0.95
V H 0.95
I H 0.95
T H 0.94
N H 0.93
W H 0.91
M H 0.88
A H 0.80
F H 0.60
L C 0.68
K C 0.80
T C 0.82
A C 0.81
H C 0.82
A C 0.84
A H 0.87
E H 0.91
E H 0.92
P H 0.94
A H 0.95
S H 0.95
L H 0.95
S H 0.96
L H 0.96
T H 0.95
E H 0.95
L H 0.93
K H 0.89
Q H 0.69
G H 0.54
I C 0.52
Y C 0.65
Q C 0.70
V C 0.67
L C 0.71
T C 0.75
L C 0.70
E C 0.72
V C 0.75
P C 0.76
Y C 0.75
L C 0.76
T C 0.82
P C 0.72
E C 0.70
Y C 0.70
R C 0.65
E C 0.64
R C 0.61
V C 0.57
L C 0.60
A C 0.62
L C 0.69
R C 0.71
E C 0.69
K C 0.74
Y C 0.76
R C 0.83
P C 0.87
T C 0.83
L C 0.80
P C 0.73
E C 0.65
A C 0.68
Q C 0.75
G C 0.79
I C 0.82
S C 0.85
G C 0.74
V C 0.71
E C 0.74
A C 0.90
END