PFRMAT SS
TARGET T0495
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0495.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0495.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0495.t04.str2.rdb  (weight 1.54758)
METHOD T0495.t04.alpha.rdb  (weight 0.659012)
METHOD T0495.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0495.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0495.t2k.str2.rdb  (weight 1.54758)
METHOD T0495.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 T0495.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0495
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 T0495.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 128
METHOD
METHOD ============================================
METHOD Comments from T0495.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0495
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 T0495.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 128
METHOD
METHOD ============================================
METHOD Comments from T0495.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0495
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 T0495.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 128
METHOD
METHOD ============================================
METHOD Comments from T0495.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0495
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 T0495.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 128
METHOD
METHOD ============================================
METHOD Comments from T0495.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0495
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 T0495.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 82
METHOD
METHOD ============================================
METHOD Comments from T0495.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0495
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 T0495.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 82
METHOD
METHOD ============================================
METHOD Comments from T0495.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0495
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 T0495.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 82
METHOD
METHOD ============================================
METHOD Comments from T0495.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0495
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 T0495.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 82
METHOD
METHOD ============================================
MODEL 1
M C 0.92
P C 0.86
M C 0.81
T C 0.61
L C 0.54
D C 0.51
L C 0.48
Q H 0.81
P H 0.91
G H 0.95
Q H 0.96
R H 0.96
L H 0.96
A H 0.95
R H 0.94
G H 0.92
V H 0.95
A H 0.96
R H 0.96
H H 0.96
L H 0.96
R H 0.94
A H 0.87
H C 0.58
G C 0.94
F C 0.82
V E 0.64
S E 0.78
V E 0.76
E E 0.70
E E 0.64
F E 0.59
V E 0.50
P C 0.82
A C 0.84
R C 0.89
G C 0.90
L C 0.74
R E 0.52
V C 0.55
D E 0.59
V E 0.86
M E 0.90
G E 0.91
L E 0.86
G C 0.78
P C 0.86
K C 0.91
G C 0.84
E C 0.53
I E 0.89
W E 0.92
V E 0.93
I E 0.93
E E 0.91
C E 0.83
K E 0.61
S C 0.72
S C 0.88
R H 0.84
A H 0.89
D H 0.88
F H 0.86
Q H 0.78
A H 0.62
D C 0.55
A C 0.54
K C 0.59
W C 0.58
Q H 0.63
G H 0.59
Y H 0.61
L H 0.62
E H 0.59
W H 0.54
C C 0.47
D C 0.51
R E 0.37
Y E 0.56
F E 0.65
W E 0.67
A C 0.49
V C 0.77
D C 0.84
M C 0.73
E C 0.76
F C 0.84
P C 0.77
A H 0.68
E H 0.71
L H 0.56
L C 0.81
P C 0.82
A C 0.72
E C 0.72
S C 0.63
G E 0.63
L E 0.89
L E 0.91
I E 0.90
A E 0.83
D C 0.54
A C 0.77
Y C 0.85
D C 0.77
A E 0.58
E E 0.85
I E 0.87
V E 0.78
R E 0.56
M C 0.69
A C 0.84
P C 0.78
E C 0.67
Q C 0.68
K C 0.75
L C 0.78
A C 0.61
P H 0.77
A H 0.90
R H 0.93
R H 0.94
K H 0.95
V H 0.96
L H 0.96
I H 0.96
Q H 0.96
K H 0.96
F H 0.96
A H 0.96
T H 0.96
H H 0.96
A H 0.96
A H 0.95
R H 0.95
R H 0.94
L H 0.92
Q H 0.90
A H 0.86
L H 0.74
R H 0.52
D C 0.85
P C 0.69
E C 0.75
G C 0.68
H C 0.73
G C 0.69
I C 0.72
F C 0.82
E C 0.91
END