PFRMAT SS
TARGET T0517
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0517.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0517.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0517.t04.str2.rdb  (weight 1.54758)
METHOD T0517.t04.alpha.rdb  (weight 0.659012)
METHOD T0517.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0517.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0517.t2k.str2.rdb  (weight 1.54758)
METHOD T0517.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 T0517.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0517
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 T0517.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 156.387
METHOD
METHOD ============================================
METHOD Comments from T0517.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0517
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 T0517.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 156.387
METHOD
METHOD ============================================
METHOD Comments from T0517.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0517
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 T0517.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 156.387
METHOD
METHOD ============================================
METHOD Comments from T0517.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0517
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 T0517.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 156.387
METHOD
METHOD ============================================
METHOD Comments from T0517.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0517
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 T0517.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 223
METHOD
METHOD ============================================
METHOD Comments from T0517.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0517
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 T0517.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 223
METHOD
METHOD ============================================
METHOD Comments from T0517.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0517
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 T0517.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 223
METHOD
METHOD ============================================
METHOD Comments from T0517.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0517
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 T0517.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 223
METHOD
METHOD ============================================
MODEL 1
M C 0.85
E C 0.80
N C 0.77
K C 0.75
K C 0.67
M E 0.69
N E 0.88
L E 0.93
L E 0.92
L E 0.87
F E 0.63
S C 0.78
G C 0.90
D C 0.84
Y H 0.84
D H 0.88
K H 0.91
A H 0.93
L H 0.94
A H 0.95
S H 0.96
L H 0.96
I H 0.96
I H 0.96
A H 0.96
N H 0.96
A H 0.96
A H 0.96
R H 0.94
E H 0.89
M C 0.64
E C 0.95
I C 0.91
E E 0.51
V E 0.84
T E 0.91
I E 0.93
F E 0.93
C E 0.89
A E 0.63
F C 0.51
W H 0.59
G H 0.73
L H 0.86
L H 0.87
L H 0.84
L H 0.77
R H 0.64
D C 0.51
P C 0.67
E C 0.66
K C 0.61
A C 0.58
S C 0.65
Q C 0.69
E C 0.70
D C 0.68
K C 0.69
S C 0.68
L C 0.60
Y C 0.57
E C 0.51
Q H 0.59
A H 0.58
F H 0.55
S H 0.53
S H 0.48
L C 0.56
T C 0.73
P C 0.79
R C 0.77
E C 0.78
A C 0.71
E C 0.64
E C 0.59
L C 0.65
P C 0.62
L C 0.59
S C 0.58
K C 0.67
M C 0.67
N C 0.77
L C 0.66
G C 0.60
G H 0.55
I H 0.67
G H 0.78
K H 0.95
K H 0.96
M H 0.96
L H 0.96
L H 0.96
E H 0.96
M H 0.95
M H 0.94
K H 0.93
E H 0.84
E C 0.57
K C 0.92
A C 0.92
P C 0.89
K C 0.84
L H 0.90
S H 0.95
D H 0.95
L H 0.95
L H 0.96
S H 0.96
G H 0.96
A H 0.95
R H 0.94
K H 0.87
K C 0.66
E C 0.94
V C 0.88
K E 0.65
F E 0.91
Y E 0.91
A E 0.87
C E 0.51
Q C 0.44
L H 0.56
S H 0.67
V H 0.77
E H 0.81
I H 0.75
M C 0.60
G C 0.91
F C 0.91
K C 0.91
K H 0.81
E H 0.85
E H 0.85
L H 0.63
F H 0.49
P C 0.51
E C 0.67
V C 0.74
Q C 0.59
I E 0.55
M E 0.44
D C 0.43
V H 0.86
K H 0.93
E H 0.94
Y H 0.93
L H 0.93
K H 0.91
N H 0.87
A H 0.82
L H 0.65
E C 0.60
S C 0.78
D C 0.88
L C 0.50
Q E 0.80
L E 0.86
F E 0.78
I C 0.69
END