PFRMAT SS
TARGET T0454
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0454.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0454.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0454.t04.str2.rdb  (weight 1.54758)
METHOD T0454.t04.alpha.rdb  (weight 0.659012)
METHOD T0454.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0454.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0454.t2k.str2.rdb  (weight 1.54758)
METHOD T0454.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 T0454.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 2180
METHOD
METHOD ============================================
METHOD Comments from T0454.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 2180
METHOD
METHOD ============================================
METHOD Comments from T0454.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 2180
METHOD
METHOD ============================================
METHOD Comments from T0454.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 2180
METHOD
METHOD ============================================
METHOD Comments from T0454.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 5302
METHOD
METHOD ============================================
METHOD Comments from T0454.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 5302
METHOD
METHOD ============================================
METHOD Comments from T0454.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 5302
METHOD
METHOD ============================================
METHOD Comments from T0454.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 5302
METHOD
METHOD ============================================
MODEL 1
M C 0.90
T C 0.80
R C 0.50
A H 0.72
D H 0.78
C H 0.83
R H 0.95
S H 0.95
R H 0.96
L H 0.96
M H 0.96
E H 0.96
V H 0.96
A H 0.96
T H 0.96
E H 0.96
L H 0.96
F H 0.96
A H 0.94
Q H 0.83
K H 0.48
G C 0.84
F C 0.83
Y C 0.71
G C 0.60
V C 0.56
S C 0.69
I H 0.94
R H 0.96
E H 0.96
L H 0.96
A H 0.96
Q H 0.93
A H 0.88
A C 0.54
G C 0.93
A C 0.90
S C 0.89
I H 0.71
S H 0.80
M H 0.83
I H 0.84
S H 0.77
Y H 0.67
H H 0.50
F C 0.71
G C 0.86
G C 0.88
K H 0.88
E H 0.94
G H 0.95
L H 0.96
Y H 0.96
A H 0.96
A H 0.96
V H 0.96
L H 0.95
Q H 0.94
E H 0.92
Q H 0.90
F H 0.89
A H 0.89
C H 0.89
F H 0.90
G H 0.91
Q H 0.90
L H 0.90
D H 0.88
D H 0.85
I H 0.78
R H 0.67
G C 0.50
Q C 0.68
A C 0.82
G C 0.88
D C 0.88
P H 0.87
L H 0.94
A H 0.95
V H 0.95
M H 0.96
T H 0.96
A H 0.96
Y H 0.96
L H 0.96
R H 0.96
W H 0.95
T H 0.95
I H 0.95
Q H 0.92
R H 0.87
H H 0.79
R H 0.67
N C 0.51
N C 0.71
P H 0.55
Q H 0.71
L H 0.85
L H 0.91
R H 0.92
F H 0.92
Y H 0.92
T H 0.92
S H 0.89
E H 0.83
L H 0.73
T H 0.55
N C 0.61
P C 0.75
T C 0.69
P H 0.79
C H 0.86
F H 0.89
A H 0.92
A H 0.93
I H 0.93
V H 0.92
S H 0.92
P H 0.91
A H 0.88
I H 0.90
A H 0.91
S H 0.92
V H 0.93
I H 0.95
R H 0.95
L H 0.95
L H 0.96
A H 0.96
E H 0.96
S H 0.96
I H 0.96
E H 0.95
A H 0.93
G H 0.90
M H 0.87
T H 0.82
R C 0.55
G C 0.88
L C 0.83
F C 0.75
R C 0.82
R C 0.76
D C 0.83
L C 0.87
H C 0.89
A H 0.92
V H 0.94
N H 0.95
S H 0.96
A H 0.96
L H 0.96
A H 0.96
L H 0.96
A H 0.96
G H 0.96
M H 0.95
V H 0.95
N H 0.93
Y H 0.92
F H 0.93
F H 0.93
L H 0.90
S H 0.87
T H 0.82
L H 0.74
A H 0.58
T C 0.63
E C 0.75
G C 0.78
L C 0.76
T C 0.76
S C 0.76
H C 0.56
S C 0.50
P H 0.74
D H 0.79
Q H 0.85
D H 0.93
E H 0.94
E H 0.95
L H 0.96
I H 0.96
R H 0.96
Q H 0.95
Y H 0.95
V H 0.95
A H 0.94
I H 0.91
F H 0.85
T H 0.73
R C 0.53
G C 0.69
I C 0.66
M C 0.74
A C 0.81
D C 0.82
G C 0.75
G C 0.72
A C 0.73
A C 0.76
P C 0.80
A C 0.88
END