PFRMAT SS
TARGET T0640
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0640.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0640.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0640.t04.str2.rdb  (weight 1.54758)
METHOD T0640.t04.alpha.rdb  (weight 0.659012)
METHOD T0640.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0640.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0640.t2k.str2.rdb  (weight 1.54758)
METHOD T0640.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 T0640.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0640
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 T0640.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 22.1141
METHOD
METHOD ============================================
METHOD Comments from T0640.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0640
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 T0640.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 22.1141
METHOD
METHOD ============================================
METHOD Comments from T0640.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0640
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 T0640.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 22.1141
METHOD
METHOD ============================================
METHOD Comments from T0640.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0640
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 T0640.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 22.1141
METHOD
METHOD ============================================
METHOD Comments from T0640.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0640
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 T0640.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 6722
METHOD
METHOD ============================================
METHOD Comments from T0640.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0640
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 T0640.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 6722
METHOD
METHOD ============================================
METHOD Comments from T0640.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0640
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 T0640.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 6722
METHOD
METHOD ============================================
METHOD Comments from T0640.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0640
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 T0640.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 6722
METHOD
METHOD ============================================
MODEL 1
M C 0.86
S C 0.76
L C 0.59
E C 0.63
K C 0.68
Q C 0.83
K C 0.91
G C 0.68
L E 0.84
A E 0.92
I E 0.92
I E 0.87
T E 0.58
G C 0.74
A C 0.76
S C 0.69
Q C 0.63
G H 0.64
I H 0.91
G H 0.95
A H 0.96
V H 0.96
I H 0.96
A H 0.96
A H 0.96
G H 0.96
L H 0.95
A H 0.94
T H 0.84
D C 0.68
G C 0.94
Y C 0.90
R E 0.52
V E 0.93
V E 0.93
L E 0.93
I E 0.88
A E 0.63
R C 0.83
S C 0.88
K H 0.75
Q H 0.86
N H 0.90
L H 0.94
E H 0.94
K H 0.95
V H 0.95
H H 0.95
D H 0.95
E H 0.94
I H 0.92
M H 0.90
R H 0.84
S H 0.72
N H 0.52
K C 0.61
H C 0.68
V C 0.84
Q C 0.82
E C 0.53
P E 0.72
I E 0.86
V E 0.91
L E 0.85
P E 0.76
L E 0.52
D C 0.64
I C 0.75
T C 0.84
D C 0.86
C H 0.85
T H 0.90
K H 0.93
A H 0.95
D H 0.95
T H 0.95
E H 0.96
I H 0.96
K H 0.95
D H 0.95
I H 0.95
H H 0.93
Q H 0.92
K H 0.83
Y C 0.54
G C 0.90
A C 0.84
V C 0.66
D C 0.54
I E 0.91
L E 0.92
V E 0.90
N E 0.79
A C 0.63
A C 0.72
A C 0.63
M C 0.56
F C 0.66
M C 0.75
D C 0.81
G C 0.84
S C 0.75
L C 0.73
S C 0.73
E C 0.83
P C 0.90
V H 0.90
D H 0.93
N H 0.93
F H 0.94
R H 0.94
K H 0.93
I H 0.93
M H 0.92
E H 0.90
I H 0.90
N H 0.84
V H 0.90
I H 0.92
A H 0.94
Q H 0.95
Y H 0.96
G H 0.96
I H 0.95
L H 0.95
K H 0.94
T H 0.91
V H 0.88
T H 0.89
E H 0.93
I H 0.94
M H 0.94
K H 0.92
V H 0.81
Q C 0.56
K C 0.88
N C 0.90
G C 0.72
Y E 0.74
I E 0.92
F E 0.90
N E 0.86
V E 0.59
A C 0.52
S C 0.54
R H 0.45
A H 0.49
A C 0.44
K C 0.51
Y C 0.61
G C 0.70
F C 0.83
A C 0.79
D C 0.80
G C 0.56
G H 0.47
I H 0.71
Y H 0.82
G H 0.88
S H 0.91
T H 0.94
K H 0.96
F H 0.96
A H 0.96
L H 0.96
L H 0.96
G H 0.95
L H 0.95
A H 0.96
E H 0.96
S H 0.96
L H 0.95
Y H 0.94
R H 0.94
E H 0.90
L H 0.86
A H 0.73
P H 0.63
L C 0.74
G C 0.90
I C 0.60
R E 0.82
V E 0.89
T E 0.88
T E 0.91
L E 0.87
C E 0.68
P C 0.63
G C 0.80
W C 0.67
V C 0.61
N C 0.65
T C 0.71
D H 0.65
M H 0.72
A H 0.74
K H 0.64
K H 0.56
A C 0.51
G C 0.71
T C 0.70
P C 0.73
F C 0.79
K C 0.78
D C 0.67
E C 0.68
E C 0.69
M C 0.81
I C 0.87
Q C 0.90
P H 0.88
D H 0.90
D H 0.92
L H 0.94
L H 0.94
N H 0.95
T H 0.96
I H 0.96
R H 0.95
C H 0.93
L H 0.86
L H 0.66
N C 0.70
L C 0.72
S H 0.50
E H 0.51
N C 0.47
V C 0.50
C C 0.49
I C 0.64
K C 0.72
D E 0.49
I E 0.81
V E 0.87
F E 0.86
E E 0.68
M C 0.73
K C 0.86
K C 0.78
S E 0.53
I E 0.75
I E 0.69
E E 0.53
G C 0.64
H C 0.61
H C 0.57
H C 0.59
H C 0.70
H C 0.80
H C 0.91
END