PFRMAT SS
TARGET T0578
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0578.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0578.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0578.t04.str2.rdb  (weight 1.54758)
METHOD T0578.t04.alpha.rdb  (weight 0.659012)
METHOD T0578.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0578.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0578.t2k.str2.rdb  (weight 1.54758)
METHOD T0578.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 T0578.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 7.82799
METHOD
METHOD ============================================
METHOD Comments from T0578.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 7.82799
METHOD
METHOD ============================================
METHOD Comments from T0578.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 7.82799
METHOD
METHOD ============================================
METHOD Comments from T0578.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 7.82799
METHOD
METHOD ============================================
METHOD Comments from T0578.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 28
METHOD
METHOD ============================================
METHOD Comments from T0578.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 28
METHOD
METHOD ============================================
METHOD Comments from T0578.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 28
METHOD
METHOD ============================================
METHOD Comments from T0578.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 28
METHOD
METHOD ============================================
MODEL 1
S C 0.67
N H 0.62
A H 0.73
M H 0.75
K H 0.76
K H 0.71
A H 0.66
T C 0.61
M H 0.71
L H 0.91
T H 0.93
Y H 0.94
L H 0.94
E H 0.94
E H 0.94
Q H 0.93
L H 0.89
E H 0.83
K H 0.66
H C 0.64
L C 0.79
G C 0.82
D C 0.81
Y C 0.67
E C 0.49
V E 0.69
G E 0.75
L E 0.67
D E 0.53
W C 0.61
D C 0.70
R C 0.75
K C 0.78
N C 0.79
H C 0.65
T E 0.76
I E 0.90
E E 0.92
V E 0.92
I E 0.93
V E 0.93
R E 0.93
L E 0.92
Y E 0.91
A E 0.86
E E 0.58
N C 0.64
N C 0.70
E C 0.73
Q C 0.53
V E 0.55
A E 0.84
I E 0.85
D E 0.82
D C 0.55
V C 0.75
D C 0.84
G C 0.79
T C 0.56
L E 0.63
S C 0.76
E C 0.78
E C 0.82
E C 0.75
F C 0.48
I E 0.66
E E 0.76
F E 0.73
E E 0.61
D E 0.64
G E 0.82
L E 0.88
L E 0.89
F E 0.82
Y E 0.58
N C 0.74
P C 0.70
Q C 0.64
K C 0.54
S C 0.72
V C 0.66
V C 0.64
D C 0.80
D H 0.62
E H 0.54
E C 0.48
Y C 0.51
L E 0.65
V E 0.81
T E 0.82
I E 0.73
P E 0.50
Y C 0.77
E C 0.78
G C 0.76
K C 0.68
K C 0.75
G C 0.82
L C 0.71
R C 0.56
K H 0.94
A H 0.95
V H 0.95
L H 0.96
D H 0.96
G H 0.96
F H 0.96
I H 0.96
H H 0.96
Y H 0.96
L H 0.96
K H 0.96
V H 0.96
V H 0.95
L H 0.94
D H 0.89
E H 0.60
G C 0.66
Q H 0.56
S H 0.71
D H 0.77
L H 0.84
L H 0.84
D H 0.79
F H 0.63
L C 0.54
S C 0.78
D C 0.88
E C 0.75
T C 0.72
A C 0.66
E C 0.66
V E 0.63
F E 0.78
E E 0.87
L E 0.83
H E 0.76
W C 0.57
E C 0.86
P H 0.86
A H 0.92
D H 0.93
F H 0.94
E H 0.94
A H 0.92
M H 0.91
I H 0.90
K H 0.85
K H 0.77
V H 0.69
A H 0.74
E H 0.72
T H 0.58
E C 0.49
K C 0.67
E C 0.72
Q C 0.72
W C 0.76
I C 0.86
A C 0.83
Y C 0.81
P C 0.82
S C 0.80
Y C 0.91
END