PFRMAT SS
TARGET T0514
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0514.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0514.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0514.t04.str2.rdb  (weight 1.54758)
METHOD T0514.t04.alpha.rdb  (weight 0.659012)
METHOD T0514.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0514.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0514.t2k.str2.rdb  (weight 1.54758)
METHOD T0514.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 T0514.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0514
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 T0514.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 205
METHOD
METHOD ============================================
METHOD Comments from T0514.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0514
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 T0514.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 205
METHOD
METHOD ============================================
METHOD Comments from T0514.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0514
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 T0514.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 205
METHOD
METHOD ============================================
METHOD Comments from T0514.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0514
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 T0514.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 205
METHOD
METHOD ============================================
METHOD Comments from T0514.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0514
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 T0514.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 84
METHOD
METHOD ============================================
METHOD Comments from T0514.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0514
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 T0514.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 84
METHOD
METHOD ============================================
METHOD Comments from T0514.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0514
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 T0514.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 84
METHOD
METHOD ============================================
METHOD Comments from T0514.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0514
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 T0514.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 84
METHOD
METHOD ============================================
MODEL 1
S C 0.82
S C 0.60
L C 0.56
T C 0.55
E C 0.50
T C 0.51
Y C 0.66
G C 0.76
L C 0.67
W E 0.56
S E 0.78
I E 0.83
N E 0.82
C E 0.76
G E 0.61
I C 0.56
Q C 0.77
E C 0.84
G C 0.86
K C 0.73
K C 0.53
V E 0.59
C E 0.66
F E 0.72
M E 0.78
H E 0.77
R E 0.79
Q E 0.77
E E 0.74
V E 0.66
N C 0.58
D C 0.80
Q C 0.89
N C 0.90
R C 0.62
V E 0.79
V E 0.88
V E 0.92
A E 0.93
M E 0.93
S E 0.93
V E 0.92
V E 0.88
L E 0.83
N C 0.55
A C 0.85
D C 0.91
G C 0.87
V C 0.61
V E 0.74
S E 0.87
G E 0.92
N E 0.92
L E 0.92
T E 0.90
V E 0.75
P C 0.56
F C 0.72
G C 0.63
I C 0.49
L E 0.51
V C 0.51
S C 0.79
K C 0.83
P C 0.82
V E 0.56
R E 0.82
L E 0.89
Q E 0.87
V E 0.74
D C 0.72
E C 0.85
G C 0.81
K C 0.77
A C 0.73
V C 0.69
I C 0.60
E C 0.53
T C 0.58
G C 0.50
I E 0.70
R E 0.76
T E 0.76
C E 0.58
V C 0.68
P C 0.81
A C 0.81
G C 0.63
C E 0.61
I E 0.84
V E 0.85
P E 0.83
I E 0.70
V E 0.49
F C 0.76
D C 0.91
K H 0.91
N H 0.94
Y H 0.95
V H 0.96
A H 0.95
A H 0.94
L H 0.91
R H 0.83
A C 0.50
G C 0.90
K C 0.87
H C 0.57
L E 0.77
K E 0.90
L E 0.92
A E 0.91
M E 0.86
T E 0.82
I E 0.64
A C 0.52
A C 0.64
P C 0.74
G C 0.80
E C 0.83
P C 0.86
P C 0.74
L C 0.50
N E 0.70
D E 0.79
L E 0.83
F E 0.85
V E 0.76
Q E 0.64
L C 0.51
N C 0.54
G C 0.57
F H 0.71
S H 0.90
N H 0.93
A H 0.94
L H 0.94
N H 0.90
R H 0.87
L H 0.79
I H 0.76
A H 0.73
L H 0.58
Q C 0.57
K C 0.90
END