PFRMAT SS
TARGET T0413
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0413.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0413.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0413.t04.str2.rdb  (weight 1.54758)
METHOD T0413.t04.alpha.rdb  (weight 0.659012)
METHOD T0413.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0413.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0413.t2k.str2.rdb  (weight 1.54758)
METHOD T0413.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 T0413.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0413
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 T0413.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 2021
METHOD
METHOD ============================================
METHOD Comments from T0413.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0413
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 T0413.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 2021
METHOD
METHOD ============================================
METHOD Comments from T0413.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0413
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 T0413.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 2021
METHOD
METHOD ============================================
METHOD Comments from T0413.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0413
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 T0413.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 2021
METHOD
METHOD ============================================
METHOD Comments from T0413.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0413
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 T0413.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 320
METHOD
METHOD ============================================
METHOD Comments from T0413.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0413
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 T0413.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 320
METHOD
METHOD ============================================
METHOD Comments from T0413.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0413
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 T0413.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 320
METHOD
METHOD ============================================
METHOD Comments from T0413.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0413
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 T0413.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 320
METHOD
METHOD ============================================
MODEL 1
S C 0.61
N H 0.51
A H 0.74
M H 0.84
K H 0.86
P H 0.90
A H 0.90
D H 0.90
L H 0.90
T H 0.89
N H 0.87
A H 0.82
D H 0.75
R H 0.69
I H 0.68
A H 0.68
L H 0.62
E H 0.60
L H 0.51
G C 0.52
H C 0.60
A C 0.68
G C 0.70
R C 0.69
N C 0.69
A C 0.55
I E 0.64
P E 0.72
Y E 0.72
L E 0.66
D E 0.51
D C 0.58
D C 0.71
R C 0.80
N C 0.83
A C 0.83
D C 0.75
R C 0.60
P E 0.62
F E 0.82
T E 0.88
L E 0.89
N E 0.88
T E 0.81
Y E 0.65
R C 0.60
P C 0.78
Y C 0.79
G C 0.82
Y C 0.81
T C 0.83
P C 0.86
D C 0.87
R C 0.82
P C 0.62
V E 0.91
V E 0.93
V E 0.93
V E 0.93
Q E 0.85
H C 0.53
G C 0.79
V C 0.78
L C 0.78
R C 0.80
N C 0.80
G H 0.72
A H 0.77
D H 0.78
Y H 0.78
R H 0.77
D H 0.74
F H 0.74
W H 0.82
I H 0.90
P H 0.92
A H 0.94
A H 0.93
D H 0.90
R H 0.77
H C 0.71
K C 0.93
L C 0.62
L E 0.87
I E 0.92
V E 0.91
A E 0.83
P E 0.51
T C 0.76
F C 0.78
S C 0.76
D C 0.77
E C 0.76
I C 0.72
W C 0.70
P C 0.66
G C 0.63
V C 0.58
E C 0.55
S C 0.54
Y C 0.57
N C 0.63
N C 0.62
G C 0.65
R C 0.63
A C 0.57
F C 0.57
T C 0.61
A C 0.61
A C 0.60
G C 0.62
N C 0.65
P C 0.67
R C 0.71
H C 0.72
V C 0.72
D C 0.72
G C 0.54
W C 0.52
T H 0.59
Y H 0.90
A H 0.92
L H 0.94
V H 0.95
A H 0.96
R H 0.96
V H 0.96
L H 0.96
A H 0.95
N H 0.95
I H 0.94
R H 0.90
A H 0.78
A H 0.58
E C 0.69
I C 0.85
A C 0.86
D C 0.87
C C 0.54
E C 0.60
Q C 0.45
V E 0.78
Y E 0.88
L E 0.91
F E 0.84
G E 0.66
H C 0.58
S C 0.73
A H 0.68
G H 0.86
G H 0.95
Q H 0.96
F H 0.96
V H 0.96
H H 0.96
R H 0.96
L H 0.95
M H 0.93
S H 0.82
S H 0.61
Q C 0.80
P C 0.65
H C 0.63
A C 0.51
P C 0.40
F E 0.57
H E 0.73
A E 0.81
V E 0.83
T E 0.81
A E 0.65
A C 0.55
N C 0.71
P C 0.70
G C 0.66
W C 0.61
Y C 0.60
T C 0.59
L C 0.64
P C 0.69
T C 0.70
F C 0.59
E C 0.57
H C 0.59
R C 0.59
F C 0.61
P C 0.56
E C 0.50
G C 0.50
L C 0.49
D C 0.52
G C 0.57
V C 0.55
G H 0.48
L H 0.54
T H 0.53
E H 0.57
D H 0.57
H H 0.55
L H 0.57
A H 0.51
R C 0.54
L C 0.67
L C 0.78
A C 0.85
Y C 0.85
P C 0.58
M E 0.90
T E 0.93
I E 0.92
L E 0.90
A E 0.61
G C 0.69
D C 0.74
Q C 0.73
D C 0.76
I C 0.75
A C 0.76
T C 0.80
D C 0.81
D C 0.49
P H 0.59
N H 0.61
L H 0.65
P H 0.77
S H 0.77
E H 0.80
P H 0.89
A H 0.91
A H 0.92
L H 0.90
R H 0.83
Q H 0.61
G C 0.62
P C 0.64
H C 0.60
R H 0.51
Y H 0.60
A H 0.58
R H 0.54
A H 0.63
R H 0.80
H H 0.87
Y H 0.91
Y H 0.93
E H 0.94
A H 0.94
G H 0.94
Q H 0.93
R H 0.91
A H 0.88
A H 0.80
A H 0.69
Q H 0.49
R C 0.71
G C 0.84
L C 0.86
P C 0.85
F C 0.65
G E 0.58
W E 0.84
Q E 0.89
L E 0.91
Q E 0.88
V E 0.86
V E 0.61
P C 0.77
G C 0.88
I C 0.79
G C 0.79
H C 0.76
D C 0.75
G C 0.53
Q H 0.58
A H 0.69
M H 0.73
S H 0.76
Q H 0.80
V H 0.83
C H 0.91
A H 0.93
S H 0.92
L H 0.92
W H 0.90
F H 0.86
D H 0.75
G C 0.48
R C 0.81
M C 0.85
P C 0.82
D C 0.78
A C 0.65
A C 0.65
E C 0.65
L C 0.71
A C 0.71
R C 0.68
L C 0.66
A C 0.68
G C 0.71
S C 0.77
Q C 0.81
S C 0.86
A C 0.91
END