PFRMAT SS
TARGET T0397
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0397.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0397.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0397.t04.str2.rdb  (weight 1.54758)
METHOD T0397.t04.alpha.rdb  (weight 0.659012)
METHOD T0397.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0397.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0397.t2k.str2.rdb  (weight 1.54758)
METHOD T0397.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 T0397.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0397
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 T0397.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 9.32066
METHOD
METHOD ============================================
METHOD Comments from T0397.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0397
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 T0397.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 9.32066
METHOD
METHOD ============================================
METHOD Comments from T0397.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0397
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 T0397.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 9.32066
METHOD
METHOD ============================================
METHOD Comments from T0397.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0397
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 T0397.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 9.32066
METHOD
METHOD ============================================
METHOD Comments from T0397.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0397
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 T0397.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 12
METHOD
METHOD ============================================
METHOD Comments from T0397.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0397
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 T0397.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 12
METHOD
METHOD ============================================
METHOD Comments from T0397.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0397
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 T0397.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 12
METHOD
METHOD ============================================
METHOD Comments from T0397.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0397
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 T0397.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 12
METHOD
METHOD ============================================
MODEL 1
M C 0.87
K C 0.80
I C 0.82
P C 0.79
K E 0.59
I E 0.84
Y E 0.88
V E 0.85
E E 0.60
G C 0.63
E C 0.65
L C 0.70
N C 0.73
D C 0.69
G C 0.64
D C 0.54
R E 0.45
V E 0.64
A E 0.66
I E 0.59
E E 0.44
K C 0.67
D C 0.71
G E 0.54
N E 0.79
A E 0.88
I E 0.86
I E 0.80
F E 0.63
L C 0.47
E C 0.51
K H 0.43
D H 0.53
E H 0.56
E H 0.51
Y C 0.54
S C 0.63
G C 0.71
N C 0.77
G C 0.73
K C 0.49
L C 0.35
L H 0.56
Y H 0.76
Q H 0.81
V H 0.82
I H 0.85
Y H 0.91
D H 0.94
D H 0.94
L H 0.94
A H 0.93
K H 0.88
Y H 0.81
M H 0.63
S C 0.49
L H 0.53
D C 0.58
T C 0.58
L C 0.62
K C 0.64
K C 0.63
D E 0.56
V E 0.86
L E 0.92
I E 0.91
Q E 0.84
Y C 0.59
P C 0.85
D C 0.89
K C 0.83
H C 0.72
T E 0.56
L E 0.76
T E 0.86
Y E 0.89
L E 0.78
K C 0.57
A C 0.87
G C 0.92
T C 0.69
K E 0.79
L E 0.88
I E 0.89
S E 0.90
V E 0.82
P E 0.68
A E 0.53
E C 0.57
G C 0.70
Y E 0.56
K E 0.81
V E 0.83
Y E 0.83
P E 0.85
I E 0.80
M E 0.74
D E 0.51
F C 0.69
G C 0.80
F C 0.67
R E 0.46
V E 0.54
L C 0.47
K C 0.65
G C 0.81
Y C 0.71
R E 0.63
L E 0.80
A E 0.85
T E 0.90
L E 0.89
E E 0.88
S E 0.71
K C 0.66
K C 0.77
G C 0.61
D E 0.66
L E 0.88
R E 0.88
Y E 0.90
V E 0.85
N E 0.76
S E 0.51
P C 0.78
V C 0.82
S C 0.81
G C 0.68
T E 0.80
V E 0.92
I E 0.92
F E 0.92
M E 0.87
N E 0.70
E C 0.54
I C 0.71
P C 0.76
S C 0.81
E C 0.83
R C 0.84
A C 0.80
N C 0.79
Y E 0.52
V E 0.82
F E 0.90
Y E 0.90
M E 0.85
L E 0.64
E C 0.73
E C 0.92
END