PFRMAT SS
TARGET T0459
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0459.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0459.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0459.t04.str2.rdb  (weight 1.54758)
METHOD T0459.t04.alpha.rdb  (weight 0.659012)
METHOD T0459.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0459.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0459.t2k.str2.rdb  (weight 1.54758)
METHOD T0459.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 T0459.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0459
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 T0459.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 212.154
METHOD
METHOD ============================================
METHOD Comments from T0459.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0459
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 T0459.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 212.154
METHOD
METHOD ============================================
METHOD Comments from T0459.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0459
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 T0459.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 212.154
METHOD
METHOD ============================================
METHOD Comments from T0459.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0459
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 T0459.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 212.154
METHOD
METHOD ============================================
METHOD Comments from T0459.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0459
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 T0459.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 875
METHOD
METHOD ============================================
METHOD Comments from T0459.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0459
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 T0459.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 875
METHOD
METHOD ============================================
METHOD Comments from T0459.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0459
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 T0459.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 875
METHOD
METHOD ============================================
METHOD Comments from T0459.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0459
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 T0459.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 875
METHOD
METHOD ============================================
MODEL 1
S C 0.67
N C 0.53
A C 0.48
M C 0.46
L C 0.49
R C 0.58
Y C 0.68
G C 0.80
D C 0.82
T C 0.71
E C 0.65
I C 0.63
C C 0.71
I C 0.72
D C 0.70
P H 0.67
S H 0.93
E H 0.95
S H 0.96
V H 0.96
L H 0.95
H H 0.94
L H 0.92
L H 0.80
G H 0.51
K C 0.62
K H 0.60
Y H 0.69
T H 0.86
M H 0.92
L H 0.94
I H 0.94
I H 0.94
S H 0.93
V H 0.92
L H 0.85
G H 0.62
N C 0.63
G C 0.75
S C 0.81
T C 0.86
R C 0.71
Q C 0.55
N C 0.60
F H 0.78
N H 0.88
D H 0.92
I H 0.93
R H 0.88
S H 0.76
S H 0.67
I C 0.66
P C 0.75
G C 0.81
I C 0.73
S C 0.76
S H 0.89
T H 0.92
I H 0.93
L H 0.94
S H 0.95
R H 0.95
R H 0.95
I H 0.95
K H 0.96
D H 0.96
L H 0.95
I H 0.94
D H 0.87
S C 0.66
G C 0.92
L C 0.79
V E 0.64
E E 0.68
R E 0.54
R C 0.66
S C 0.85
G C 0.90
Q C 0.84
I E 0.61
T E 0.84
T E 0.89
Y E 0.89
A E 0.85
L E 0.64
T C 0.81
E C 0.66
K C 0.62
G H 0.53
M H 0.65
N H 0.65
V H 0.86
R H 0.92
N H 0.94
S H 0.95
L H 0.95
M H 0.95
P H 0.96
L H 0.95
L H 0.96
Q H 0.95
Y H 0.93
I H 0.91
S H 0.88
V H 0.79
L H 0.60
D C 0.69
R C 0.76
N C 0.79
G C 0.83
D C 0.90
END