PFRMAT SS
TARGET T0440
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0440.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0440.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0440.t04.str2.rdb  (weight 1.54758)
METHOD T0440.t04.alpha.rdb  (weight 0.659012)
METHOD T0440.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0440.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0440.t2k.str2.rdb  (weight 1.54758)
METHOD T0440.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 T0440.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0440
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 T0440.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 1471
METHOD
METHOD ============================================
METHOD Comments from T0440.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0440
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 T0440.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 1471
METHOD
METHOD ============================================
METHOD Comments from T0440.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0440
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 T0440.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 1471
METHOD
METHOD ============================================
METHOD Comments from T0440.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0440
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 T0440.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 1471
METHOD
METHOD ============================================
METHOD Comments from T0440.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0440
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 T0440.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 217
METHOD
METHOD ============================================
METHOD Comments from T0440.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0440
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 T0440.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 217
METHOD
METHOD ============================================
METHOD Comments from T0440.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0440
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 T0440.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 217
METHOD
METHOD ============================================
METHOD Comments from T0440.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0440
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 T0440.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 217
METHOD
METHOD ============================================
MODEL 1
M C 0.88
K C 0.80
R C 0.68
D C 0.67
G C 0.57
H C 0.47
T E 0.46
H C 0.60
T C 0.77
E C 0.77
F C 0.75
C C 0.81
P C 0.68
H C 0.69
G C 0.65
T C 0.73
H C 0.79
D C 0.84
D C 0.81
V H 0.94
E H 0.95
E H 0.96
M H 0.96
V H 0.96
L H 0.96
K H 0.96
A H 0.95
I H 0.94
E H 0.89
L C 0.62
D C 0.93
F C 0.89
D C 0.56
E E 0.88
Y E 0.92
S E 0.92
I E 0.85
V E 0.56
E C 0.68
H C 0.74
A C 0.78
P C 0.77
L C 0.76
S C 0.75
S C 0.65
E C 0.61
F C 0.60
M C 0.66
K C 0.71
N C 0.75
T C 0.72
A H 0.51
G H 0.51
D H 0.53
K H 0.54
E H 0.48
A H 0.50
V C 0.50
T C 0.49
T H 0.49
A H 0.62
S H 0.59
M H 0.54
A C 0.51
M H 0.77
S H 0.77
D H 0.73
L H 0.86
P H 0.93
Y H 0.94
Y H 0.95
F H 0.96
K H 0.96
K H 0.95
M H 0.96
N H 0.96
H H 0.95
I H 0.95
K H 0.94
K H 0.92
K H 0.86
Y H 0.70
A C 0.50
S C 0.75
D C 0.82
L C 0.67
L E 0.62
I E 0.88
H E 0.87
I E 0.85
G E 0.83
F E 0.84
E E 0.83
V E 0.74
D E 0.66
Y C 0.50
L C 0.73
I C 0.74
G C 0.72
Y C 0.55
E H 0.74
D H 0.84
F H 0.87
T H 0.90
R H 0.91
D H 0.91
F H 0.90
L H 0.86
N H 0.80
E H 0.66
Y C 0.58
G C 0.83
P C 0.83
Q C 0.78
T C 0.79
D C 0.72
D E 0.90
G E 0.93
V E 0.92
L E 0.87
S E 0.63
L E 0.51
H E 0.52
F E 0.56
L C 0.49
E C 0.70
G C 0.78
Q C 0.74
G C 0.70
G C 0.63
F C 0.63
R C 0.61
S C 0.51
I H 0.58
D H 0.62
F H 0.59
S H 0.60
A H 0.72
E H 0.78
D H 0.80
Y H 0.82
N H 0.82
E H 0.74
G H 0.64
I H 0.66
V H 0.69
Q H 0.66
F H 0.69
Y H 0.63
G H 0.55
G C 0.54
F C 0.59
E C 0.58
Q C 0.55
A H 0.53
Q H 0.90
L H 0.94
A H 0.95
Y H 0.95
L H 0.95
E H 0.95
G H 0.94
V H 0.94
K H 0.95
Q H 0.95
S H 0.96
I H 0.96
E H 0.96
A H 0.95
D H 0.95
L H 0.92
G H 0.85
L H 0.54
F C 0.82
K C 0.89
P C 0.78
R C 0.50
R E 0.85
M E 0.84
G E 0.78
H E 0.52
I C 0.53
S H 0.46
L H 0.60
C H 0.61
Q H 0.58
K H 0.54
F C 0.48
Q C 0.71
Q C 0.71
F C 0.73
F C 0.72
G C 0.68
E C 0.55
D C 0.53
T H 0.48
S C 0.49
D C 0.50
F C 0.61
S H 0.64
E H 0.82
E H 0.85
V H 0.90
M H 0.94
E H 0.95
K H 0.95
F H 0.96
R H 0.96
V H 0.96
I H 0.96
L H 0.96
A H 0.96
L H 0.96
V H 0.96
K H 0.94
K H 0.89
R C 0.62
D C 0.94
Y C 0.84
E E 0.78
L E 0.88
D E 0.91
F E 0.88
N E 0.69
T C 0.61
A C 0.69
G C 0.59
L C 0.51
F C 0.59
K C 0.64
P C 0.67
L C 0.67
C C 0.70
G C 0.80
E C 0.81
T C 0.73
Y C 0.82
P C 0.88
P C 0.85
K H 0.92
K H 0.94
I H 0.95
V H 0.96
T H 0.96
L H 0.96
A H 0.96
S H 0.95
E H 0.90
L C 0.63
Q C 0.94
I C 0.92
P C 0.55
F E 0.85
V E 0.89
Y E 0.82
G E 0.52
S C 0.77
D C 0.78
S C 0.73
H C 0.77
G C 0.80
V H 0.66
Q H 0.73
D H 0.76
I H 0.74
G H 0.64
R H 0.62
G H 0.58
Y H 0.86
S H 0.90
T H 0.90
Y H 0.86
C H 0.68
Q H 0.49
K C 0.88
END