PFRMAT SS
TARGET T0627
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0627.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0627.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0627.t04.str2.rdb  (weight 1.54758)
METHOD T0627.t04.alpha.rdb  (weight 0.659012)
METHOD T0627.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0627.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0627.t2k.str2.rdb  (weight 1.54758)
METHOD T0627.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 T0627.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 1054
METHOD
METHOD ============================================
METHOD Comments from T0627.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 1054
METHOD
METHOD ============================================
METHOD Comments from T0627.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 1054
METHOD
METHOD ============================================
METHOD Comments from T0627.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 1054
METHOD
METHOD ============================================
METHOD Comments from T0627.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 45
METHOD
METHOD ============================================
METHOD Comments from T0627.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 45
METHOD
METHOD ============================================
METHOD Comments from T0627.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 45
METHOD
METHOD ============================================
METHOD Comments from T0627.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 45
METHOD
METHOD ============================================
MODEL 1
M C 0.87
I C 0.76
D C 0.64
T C 0.50
F H 0.48
E H 0.44
R C 0.47
T C 0.60
G C 0.76
P C 0.68
L C 0.47
M C 0.41
E C 0.43
A C 0.60
S C 0.77
S C 0.79
Y C 0.84
P H 0.79
A H 0.92
W H 0.94
A H 0.95
Q H 0.95
Q H 0.95
L H 0.94
I H 0.93
N H 0.88
D H 0.71
C H 0.62
S H 0.50
P H 0.88
A H 0.92
K H 0.92
A H 0.91
R H 0.88
V H 0.82
V H 0.64
E C 0.54
H C 0.67
E H 0.89
L H 0.93
Y H 0.94
Q H 0.93
Q H 0.92
M H 0.87
R H 0.75
D C 0.67
A C 0.89
K C 0.88
L C 0.78
S C 0.92
P H 0.92
Q H 0.95
I H 0.95
M H 0.95
R H 0.95
Q H 0.95
Y H 0.94
L H 0.92
I H 0.90
G H 0.83
G H 0.78
W H 0.86
P H 0.90
V H 0.92
V H 0.93
E H 0.91
Q H 0.83
F H 0.83
A H 0.92
V H 0.95
Y H 0.95
M H 0.94
A H 0.93
K H 0.93
N H 0.91
L H 0.87
T H 0.67
K C 0.52
T C 0.74
R C 0.69
F C 0.66
G C 0.58
R C 0.65
H C 0.67
P H 0.49
G C 0.53
E H 0.74
D H 0.90
M H 0.93
A H 0.94
R H 0.95
R H 0.94
W H 0.93
L H 0.92
M H 0.90
R H 0.85
N H 0.73
I H 0.68
R H 0.63
V H 0.59
E H 0.57
L H 0.67
N H 0.60
H H 0.71
A H 0.92
D H 0.94
Y H 0.95
W H 0.95
V H 0.96
N H 0.96
W H 0.96
C H 0.95
A H 0.94
A H 0.87
H C 0.50
D C 0.92
V C 0.90
T C 0.92
L H 0.91
E H 0.93
D H 0.94
L H 0.93
H H 0.85
D H 0.53
Q C 0.77
R C 0.86
V C 0.87
A C 0.85
P H 0.90
E H 0.93
L H 0.94
H H 0.95
A H 0.95
L H 0.95
S H 0.95
H H 0.94
W H 0.93
C H 0.92
W H 0.90
Q H 0.86
T H 0.71
S C 0.57
S C 0.71
S C 0.69
D C 0.75
S C 0.58
L H 0.93
A H 0.95
V H 0.95
A H 0.95
M H 0.95
A H 0.95
A H 0.93
T H 0.92
N H 0.91
Y H 0.92
A H 0.90
I H 0.89
E H 0.82
G H 0.65
A H 0.58
T H 0.61
G H 0.79
E H 0.89
W H 0.90
S H 0.90
A H 0.86
V H 0.82
V H 0.77
C H 0.70
S H 0.62
T H 0.47
G H 0.53
V H 0.51
Y H 0.51
A H 0.44
E C 0.50
A C 0.69
F C 0.79
A C 0.76
E C 0.52
E C 0.54
T C 0.60
R C 0.68
K H 0.72
K H 0.90
S H 0.93
M H 0.95
K H 0.96
W H 0.95
L H 0.95
K H 0.95
M H 0.93
H H 0.86
A H 0.75
Q H 0.61
Y H 0.61
D C 0.53
D C 0.51
A C 0.50
H C 0.67
P H 0.77
W H 0.88
E H 0.91
A H 0.94
L H 0.95
E H 0.95
I H 0.96
I H 0.96
C H 0.95
T H 0.94
L H 0.89
V H 0.70
G C 0.62
N C 0.77
K C 0.86
P C 0.76
S C 0.69
L H 0.87
Q H 0.91
L H 0.93
Q H 0.95
A H 0.96
E H 0.96
L H 0.96
R H 0.96
Q H 0.96
A H 0.96
V H 0.96
T H 0.95
K H 0.94
S H 0.95
Y H 0.95
D H 0.95
Y H 0.95
M H 0.95
Y H 0.95
L H 0.94
F H 0.93
L H 0.93
E H 0.90
R H 0.80
C H 0.62
I C 0.52
Q C 0.72
L C 0.53
D C 0.54
K C 0.53
V C 0.63
K C 0.68
S C 0.71
P C 0.65
R C 0.61
G C 0.47
R E 0.48
V E 0.57
A E 0.58
A E 0.60
L E 0.53
E C 0.60
M C 0.91
END