PFRMAT SS
TARGET T0389
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0389.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0389.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0389.t04.str2.rdb  (weight 1.54758)
METHOD T0389.t04.alpha.rdb  (weight 0.659012)
METHOD T0389.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0389.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0389.t2k.str2.rdb  (weight 1.54758)
METHOD T0389.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 T0389.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 2363
METHOD
METHOD ============================================
METHOD Comments from T0389.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 2363
METHOD
METHOD ============================================
METHOD Comments from T0389.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 2363
METHOD
METHOD ============================================
METHOD Comments from T0389.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 2363
METHOD
METHOD ============================================
METHOD Comments from T0389.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 510
METHOD
METHOD ============================================
METHOD Comments from T0389.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 510
METHOD
METHOD ============================================
METHOD Comments from T0389.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 510
METHOD
METHOD ============================================
METHOD Comments from T0389.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 510
METHOD
METHOD ============================================
MODEL 1
M C 0.90
I C 0.79
G C 0.81
T H 0.54
Q H 0.63
I H 0.68
V H 0.69
T H 0.89
E H 0.92
R H 0.92
L H 0.92
V H 0.91
A H 0.88
L H 0.87
L H 0.82
E H 0.76
S H 0.55
G C 0.76
T C 0.84
E C 0.86
K C 0.82
V E 0.74
L E 0.91
L E 0.92
I E 0.90
D E 0.81
S C 0.55
R C 0.81
P C 0.86
F H 0.67
V H 0.78
E H 0.82
Y H 0.77
N H 0.67
T C 0.49
S C 0.68
H C 0.72
I C 0.75
L C 0.71
E C 0.74
A C 0.62
I E 0.51
N E 0.54
I C 0.61
N C 0.79
C H 0.59
S H 0.79
K H 0.85
L H 0.88
M H 0.85
K H 0.80
R H 0.73
R H 0.68
L H 0.61
Q H 0.53
Q C 0.58
D C 0.64
K C 0.50
V H 0.47
L H 0.51
I H 0.58
T H 0.58
E H 0.52
L H 0.45
I C 0.50
Q C 0.61
H C 0.48
S H 0.54
A H 0.59
K H 0.59
H H 0.55
K H 0.53
V H 0.48
D C 0.55
I C 0.64
D C 0.74
C C 0.79
S C 0.86
Q C 0.77
K E 0.61
V E 0.90
V E 0.92
V E 0.91
Y E 0.85
D C 0.56
Q C 0.84
S C 0.87
S C 0.82
Q C 0.73
D C 0.59
V C 0.55
A C 0.53
S H 0.53
L H 0.55
S H 0.60
S H 0.72
D H 0.76
C H 0.82
F H 0.90
L H 0.92
T H 0.94
V H 0.94
L H 0.94
L H 0.94
G H 0.93
K H 0.92
L H 0.87
E H 0.76
K C 0.59
S C 0.88
F C 0.87
N C 0.79
S C 0.59
V E 0.80
H E 0.88
L E 0.89
L E 0.77
A C 0.53
G C 0.76
G C 0.66
F H 0.83
A H 0.92
E H 0.94
F H 0.94
S H 0.92
R H 0.85
C H 0.71
F C 0.66
P C 0.57
G H 0.51
L H 0.52
C C 0.62
E C 0.71
G C 0.79
K C 0.81
S C 0.79
T C 0.76
L C 0.77
V C 0.77
P C 0.79
T C 0.79
C C 0.78
I C 0.76
S C 0.78
Q C 0.82
P C 0.83
A C 0.77
H C 0.76
H C 0.76
H C 0.73
H C 0.75
H C 0.80
H C 0.91
END