PFRMAT SS
TARGET T0503
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0503.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0503.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0503.t04.str2.rdb  (weight 1.54758)
METHOD T0503.t04.alpha.rdb  (weight 0.659012)
METHOD T0503.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0503.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0503.t2k.str2.rdb  (weight 1.54758)
METHOD T0503.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 T0503.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0503
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 T0503.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 2115
METHOD
METHOD ============================================
METHOD Comments from T0503.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0503
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 T0503.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 2115
METHOD
METHOD ============================================
METHOD Comments from T0503.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0503
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 T0503.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 2115
METHOD
METHOD ============================================
METHOD Comments from T0503.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0503
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 T0503.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 2115
METHOD
METHOD ============================================
METHOD Comments from T0503.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0503
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 T0503.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 458
METHOD
METHOD ============================================
METHOD Comments from T0503.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0503
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 T0503.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 458
METHOD
METHOD ============================================
METHOD Comments from T0503.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0503
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 T0503.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 458
METHOD
METHOD ============================================
METHOD Comments from T0503.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0503
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 T0503.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 458
METHOD
METHOD ============================================
MODEL 1
M C 0.72
H H 0.65
T H 0.81
A H 0.85
L H 0.86
I H 0.87
N H 0.82
H H 0.69
I C 0.53
R C 0.59
K C 0.55
F C 0.54
I C 0.69
F C 0.81
L C 0.90
T C 0.93
D H 0.92
E H 0.94
D H 0.94
A H 0.96
G H 0.95
T H 0.94
L H 0.93
S H 0.91
A H 0.79
F C 0.49
F C 0.66
Q C 0.54
L E 0.72
K E 0.78
K E 0.83
V E 0.55
R C 0.80
K C 0.91
K C 0.92
E C 0.51
T E 0.83
L E 0.88
L E 0.83
K E 0.61
T C 0.76
G C 0.88
E C 0.71
I C 0.55
C C 0.59
R C 0.60
I E 0.68
N E 0.87
Y E 0.91
F E 0.93
V E 0.90
V E 0.84
K E 0.59
G C 0.52
C E 0.80
L E 0.90
R E 0.91
L E 0.92
F E 0.91
F E 0.89
I E 0.86
D C 0.62
E C 0.87
K C 0.94
G C 0.91
I C 0.67
E E 0.88
Q E 0.88
T E 0.91
T E 0.88
Q E 0.88
F E 0.87
A E 0.78
I C 0.59
E C 0.85
N C 0.89
W C 0.65
W E 0.54
L E 0.57
S E 0.42
D H 0.49
Y H 0.66
M H 0.73
A H 0.71
F H 0.68
Q H 0.57
K C 0.64
Q C 0.84
Q C 0.84
P C 0.77
A C 0.70
D C 0.45
F E 0.50
Y E 0.67
I E 0.78
Q E 0.82
S E 0.78
V E 0.68
E E 0.57
N E 0.48
C E 0.69
E E 0.87
L E 0.91
L E 0.90
S E 0.89
I E 0.70
T C 0.63
Y H 0.81
T H 0.91
E H 0.93
Q H 0.95
E H 0.95
N H 0.95
L H 0.94
F H 0.92
E H 0.78
R H 0.62
I C 0.75
P H 0.81
A H 0.88
L H 0.93
E H 0.95
R H 0.95
Y H 0.96
F H 0.96
R H 0.96
L H 0.96
V H 0.96
Y H 0.95
Q H 0.95
K H 0.95
S H 0.94
F H 0.95
A H 0.94
A H 0.94
A H 0.94
Q H 0.95
L H 0.94
R H 0.94
S H 0.94
K H 0.94
F H 0.90
Q H 0.80
H H 0.62
M C 0.62
Y C 0.83
S C 0.88
K H 0.93
E H 0.95
E H 0.95
Q H 0.96
Y H 0.96
H H 0.96
N H 0.96
F H 0.95
S H 0.94
S H 0.86
R H 0.72
F C 0.76
P C 0.68
E C 0.59
F H 0.46
I C 0.47
Q C 0.47
R C 0.53
V C 0.73
P C 0.79
Q H 0.90
Y H 0.92
L H 0.92
L H 0.93
A H 0.93
S H 0.90
Y H 0.85
L C 0.49
G C 0.87
F C 0.89
T C 0.92
P H 0.90
E H 0.93
Y H 0.94
L H 0.96
S H 0.96
E H 0.96
I H 0.96
R H 0.95
K H 0.91
K H 0.85
Y H 0.72
I H 0.53
S C 0.88
END