PFRMAT SS
TARGET T0520
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0520.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0520.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0520.t04.str2.rdb  (weight 1.54758)
METHOD T0520.t04.alpha.rdb  (weight 0.659012)
METHOD T0520.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0520.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0520.t2k.str2.rdb  (weight 1.54758)
METHOD T0520.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 T0520.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 533.191
METHOD
METHOD ============================================
METHOD Comments from T0520.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 533.191
METHOD
METHOD ============================================
METHOD Comments from T0520.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 533.191
METHOD
METHOD ============================================
METHOD Comments from T0520.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 533.191
METHOD
METHOD ============================================
METHOD Comments from T0520.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 2516
METHOD
METHOD ============================================
METHOD Comments from T0520.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 2516
METHOD
METHOD ============================================
METHOD Comments from T0520.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 2516
METHOD
METHOD ============================================
METHOD Comments from T0520.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 2516
METHOD
METHOD ============================================
MODEL 1
S C 0.81
N C 0.75
A C 0.75
E C 0.68
R C 0.57
R C 0.54
L E 0.62
C E 0.84
A E 0.89
I E 0.91
L E 0.90
A E 0.84
A E 0.67
D C 0.46
M C 0.48
A C 0.46
G C 0.47
Y H 0.61
S H 0.71
R H 0.83
L H 0.85
M H 0.81
E H 0.67
R C 0.58
N C 0.79
E C 0.90
T H 0.91
D H 0.94
V H 0.95
L H 0.96
N H 0.96
R H 0.96
Q H 0.96
K H 0.96
L H 0.95
Y H 0.95
R H 0.95
R H 0.95
E H 0.94
L H 0.94
I H 0.95
D H 0.95
P H 0.96
A H 0.96
I H 0.95
A H 0.92
Q H 0.82
A C 0.56
G C 0.92
G C 0.78
Q E 0.71
I E 0.83
V E 0.80
K E 0.79
T E 0.75
T E 0.54
G C 0.56
D C 0.57
G E 0.72
M E 0.79
L E 0.79
A E 0.76
R E 0.61
F C 0.59
D C 0.81
T C 0.86
A C 0.79
Q C 0.63
A C 0.57
A H 0.60
L H 0.83
R H 0.88
C H 0.92
A H 0.95
L H 0.96
E H 0.96
I H 0.96
Q H 0.96
Q H 0.96
A H 0.95
M H 0.95
Q H 0.94
Q H 0.92
R H 0.87
E H 0.83
E H 0.76
D H 0.61
T C 0.60
P C 0.73
R C 0.78
K C 0.82
E C 0.82
R C 0.71
I E 0.55
Q E 0.79
Y E 0.89
R E 0.90
I E 0.89
G E 0.84
I E 0.78
N E 0.63
I C 0.49
G C 0.61
D C 0.49
I E 0.67
V E 0.74
L E 0.65
E E 0.51
D E 0.48
G C 0.62
D C 0.70
I C 0.60
F C 0.57
G C 0.62
D H 0.56
A H 0.77
V H 0.91
N H 0.92
V H 0.95
A H 0.95
A H 0.95
R H 0.94
L H 0.93
E H 0.91
A H 0.86
I H 0.70
S C 0.67
E C 0.86
P C 0.84
G C 0.85
A E 0.51
I E 0.85
C E 0.87
V E 0.68
S C 0.79
D H 0.90
I H 0.94
V H 0.94
H H 0.94
Q H 0.93
I H 0.88
T H 0.74
Q H 0.62
D C 0.49
R C 0.57
V C 0.69
S C 0.75
E C 0.59
P E 0.56
F E 0.67
T E 0.63
D E 0.56
L C 0.60
G C 0.69
L E 0.50
Q E 0.78
K E 0.81
V E 0.70
K C 0.52
N C 0.76
I C 0.78
T C 0.81
R C 0.77
P C 0.57
I E 0.75
R E 0.87
V E 0.90
W E 0.90
Q E 0.89
W E 0.76
V C 0.58
P C 0.81
D C 0.81
A C 0.80
D C 0.75
R C 0.76
D C 0.76
Q C 0.78
S C 0.83
H C 0.84
D C 0.84
P C 0.83
Q C 0.82
P C 0.70
S C 0.68
H C 0.71
V C 0.72
Q C 0.82
H C 0.91
END