PFRMAT SS
TARGET T0399
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0399.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0399.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0399.t04.str2.rdb  (weight 1.54758)
METHOD T0399.t04.alpha.rdb  (weight 0.659012)
METHOD T0399.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0399.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0399.t2k.str2.rdb  (weight 1.54758)
METHOD T0399.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 T0399.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 132
METHOD
METHOD ============================================
METHOD Comments from T0399.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 132
METHOD
METHOD ============================================
METHOD Comments from T0399.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 132
METHOD
METHOD ============================================
METHOD Comments from T0399.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 132
METHOD
METHOD ============================================
METHOD Comments from T0399.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 29
METHOD
METHOD ============================================
METHOD Comments from T0399.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 29
METHOD
METHOD ============================================
METHOD Comments from T0399.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 29
METHOD
METHOD ============================================
METHOD Comments from T0399.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0399
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 T0399.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 29
METHOD
METHOD ============================================
MODEL 1
M C 0.87
S C 0.74
M C 0.60
K H 0.50
K H 0.52
T H 0.59
K H 0.70
N H 0.84
W H 0.92
L H 0.95
L H 0.96
V H 0.96
F H 0.96
L H 0.96
T H 0.96
V H 0.96
T H 0.96
F H 0.95
C H 0.95
F H 0.94
L H 0.91
M H 0.87
L H 0.73
G H 0.48
C C 0.66
Q C 0.78
S C 0.79
K C 0.77
E C 0.76
D C 0.74
K C 0.71
K C 0.69
G C 0.68
G C 0.69
T C 0.60
K C 0.59
P C 0.58
S C 0.52
N C 0.52
E H 0.48
A H 0.57
A H 0.54
L H 0.47
T C 0.50
K C 0.48
T H 0.54
E H 0.55
N H 0.51
L H 0.70
D H 0.67
F H 0.66
R H 0.51
L C 0.53
S C 0.61
F C 0.58
N C 0.61
K C 0.46
I E 0.46
K E 0.54
V E 0.46
T E 0.39
T E 0.43
D E 0.46
Q E 0.40
N C 0.42
H C 0.47
F C 0.51
S C 0.59
G C 0.76
G C 0.85
T C 0.78
S C 0.80
I H 0.94
E H 0.95
Q H 0.95
L H 0.95
K H 0.94
Q H 0.92
W H 0.84
F H 0.52
G C 0.84
D C 0.88
P C 0.76
N C 0.74
K C 0.69
S C 0.71
E C 0.71
Q C 0.66
R C 0.47
N C 0.47
A C 0.54
G C 0.76
N C 0.70
I E 0.71
T E 0.86
L E 0.89
D E 0.88
S E 0.89
Y E 0.91
T E 0.90
W E 0.88
V E 0.72
K C 0.63
D C 0.85
G C 0.78
A E 0.65
V E 0.89
I E 0.92
N E 0.93
A E 0.93
Q E 0.92
L E 0.88
Y E 0.61
K C 0.88
N C 0.90
S E 0.52
T E 0.83
V E 0.84
A E 0.79
R E 0.60
S E 0.46
I H 0.40
S C 0.57
N C 0.77
F C 0.72
S C 0.62
F C 0.64
S C 0.69
R C 0.66
E C 0.69
A C 0.75
K C 0.74
I C 0.72
G C 0.85
K H 0.88
E H 0.90
D H 0.91
Y H 0.93
D H 0.91
E H 0.86
L H 0.81
K H 0.67
I C 0.63
G C 0.90
E C 0.85
S C 0.82
Y H 0.93
K H 0.95
K H 0.95
V H 0.95
V H 0.95
E H 0.93
K H 0.86
L H 0.60
G C 0.80
E C 0.87
P C 0.76
D C 0.72
V C 0.63
L C 0.54
S C 0.45
Q E 0.38
S C 0.39
M C 0.45
S C 0.56
S C 0.76
D C 0.83
K C 0.68
E C 0.47
E E 0.71
M E 0.83
Q E 0.88
T E 0.91
V E 0.90
W E 0.89
S E 0.82
S E 0.63
G E 0.49
I E 0.53
K E 0.49
T C 0.63
K C 0.80
S C 0.81
S C 0.78
S C 0.74
A C 0.59
T E 0.69
I E 0.86
E E 0.92
L E 0.92
Y E 0.92
F E 0.90
E E 0.73
N C 0.89
G C 0.88
L E 0.65
L E 0.88
K E 0.82
N E 0.79
K E 0.53
T C 0.44
Q C 0.49
K C 0.67
D C 0.76
L C 0.86
E C 0.92
END