PFRMAT SS
TARGET T0412
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0412.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0412.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0412.t04.str2.rdb  (weight 1.54758)
METHOD T0412.t04.alpha.rdb  (weight 0.659012)
METHOD T0412.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0412.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0412.t2k.str2.rdb  (weight 1.54758)
METHOD T0412.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 T0412.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0412
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 T0412.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 1764
METHOD
METHOD ============================================
METHOD Comments from T0412.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0412
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 T0412.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 1764
METHOD
METHOD ============================================
METHOD Comments from T0412.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0412
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 T0412.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 1764
METHOD
METHOD ============================================
METHOD Comments from T0412.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0412
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 T0412.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 1764
METHOD
METHOD ============================================
METHOD Comments from T0412.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0412
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 T0412.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 365
METHOD
METHOD ============================================
METHOD Comments from T0412.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0412
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 T0412.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 365
METHOD
METHOD ============================================
METHOD Comments from T0412.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0412
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 T0412.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 365
METHOD
METHOD ============================================
METHOD Comments from T0412.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0412
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 T0412.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 365
METHOD
METHOD ============================================
MODEL 1
S C 0.80
N C 0.69
A C 0.73
L C 0.76
F C 0.73
S H 0.81
S H 0.87
R H 0.89
D H 0.88
I H 0.85
L H 0.89
E H 0.94
V H 0.95
L H 0.96
Q H 0.96
D H 0.96
I H 0.96
H H 0.95
M H 0.91
E H 0.83
T C 0.48
G C 0.92
E C 0.83
T E 0.57
V E 0.80
A E 0.88
I E 0.88
A E 0.88
T E 0.87
K E 0.72
N C 0.67
D C 0.87
I C 0.78
Y E 0.79
L E 0.92
Q E 0.93
Y E 0.93
I E 0.92
Q E 0.89
I E 0.83
I E 0.75
E E 0.56
S C 0.67
V C 0.75
H C 0.75
A C 0.53
L E 0.68
R E 0.80
F E 0.79
H E 0.73
V E 0.56
D C 0.67
E C 0.81
N C 0.88
A C 0.72
I E 0.52
R E 0.50
P C 0.52
L C 0.47
T C 0.45
M C 0.47
S C 0.52
S H 0.56
N H 0.69
G H 0.71
W H 0.78
M H 0.78
L H 0.79
M H 0.74
S H 0.53
T C 0.70
M C 0.90
N C 0.92
D H 0.89
K H 0.93
A H 0.95
I H 0.95
D H 0.95
N H 0.95
T H 0.94
V H 0.92
R H 0.81
R H 0.62
A C 0.63
N C 0.78
T C 0.73
I C 0.70
T C 0.68
Q C 0.75
K C 0.85
D C 0.72
G C 0.77
I C 0.74
R C 0.74
F C 0.77
E C 0.84
V H 0.94
D H 0.95
D H 0.95
M H 0.96
M H 0.96
A H 0.95
R H 0.95
I H 0.96
R H 0.95
Q H 0.95
V H 0.94
R H 0.93
E H 0.86
Q H 0.50
G C 0.84
Y C 0.74
A C 0.50
S C 0.48
A C 0.60
E C 0.53
H C 0.54
I C 0.49
P C 0.59
F C 0.67
V C 0.73
G C 0.78
G E 0.54
G E 0.78
T E 0.89
I E 0.90
C E 0.89
V E 0.85
L E 0.83
L E 0.72
P E 0.66
M C 0.74
T C 0.85
I C 0.91
Q C 0.91
G C 0.72
Q E 0.77
P E 0.87
V E 0.92
T E 0.92
M E 0.92
G E 0.91
L E 0.82
G E 0.61
G C 0.64
A C 0.65
L C 0.52
D C 0.52
R C 0.61
I C 0.79
K C 0.86
Q H 0.83
N H 0.84
Y H 0.88
D H 0.90
R H 0.89
Y H 0.87
L H 0.89
E H 0.94
L H 0.95
L H 0.95
L H 0.96
N H 0.95
G H 0.95
V H 0.95
Q H 0.95
Q H 0.94
L H 0.94
K H 0.93
K H 0.91
S H 0.86
D H 0.76
S C 0.54
F C 0.86
H C 0.83
Q C 0.80
P C 0.83
I C 0.91
END