PFRMAT SS
TARGET T0557
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0557.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0557.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0557.t04.str2.rdb  (weight 1.54758)
METHOD T0557.t04.alpha.rdb  (weight 0.659012)
METHOD T0557.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0557.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0557.t2k.str2.rdb  (weight 1.54758)
METHOD T0557.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 T0557.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0557
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 T0557.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 876
METHOD
METHOD ============================================
METHOD Comments from T0557.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0557
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 T0557.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 876
METHOD
METHOD ============================================
METHOD Comments from T0557.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0557
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 T0557.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 876
METHOD
METHOD ============================================
METHOD Comments from T0557.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0557
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 T0557.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 876
METHOD
METHOD ============================================
METHOD Comments from T0557.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0557
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 T0557.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 164
METHOD
METHOD ============================================
METHOD Comments from T0557.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0557
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 T0557.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 164
METHOD
METHOD ============================================
METHOD Comments from T0557.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0557
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 T0557.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 164
METHOD
METHOD ============================================
METHOD Comments from T0557.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0557
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 T0557.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 164
METHOD
METHOD ============================================
MODEL 1
M C 0.86
R C 0.67
S H 0.59
A H 0.88
T H 0.92
D H 0.94
L H 0.95
L H 0.95
D H 0.95
E H 0.94
L H 0.93
N H 0.88
A H 0.69
V C 0.67
D C 0.87
E C 0.81
S C 0.73
A C 0.59
R E 0.45
I E 0.57
E E 0.65
A E 0.62
K E 0.50
R C 0.39
A C 0.64
S C 0.83
D C 0.87
M C 0.86
G C 0.77
K H 0.56
S H 0.60
V H 0.79
M H 0.75
E H 0.77
T H 0.75
V H 0.75
I H 0.73
A H 0.70
F H 0.52
A C 0.40
N C 0.68
E C 0.82
P C 0.85
G C 0.87
L C 0.81
D C 0.82
G C 0.77
G C 0.62
Y E 0.82
L E 0.91
L E 0.92
L E 0.88
G E 0.85
V E 0.78
D E 0.66
W C 0.54
A C 0.76
I C 0.85
N C 0.83
D E 0.57
K E 0.79
G E 0.77
D E 0.68
T E 0.55
V C 0.52
Y C 0.63
R C 0.75
P C 0.77
V C 0.78
G C 0.76
L C 0.48
P H 0.58
D H 0.62
P H 0.85
D H 0.89
K H 0.92
V H 0.93
Q H 0.93
R H 0.92
D H 0.89
L H 0.87
A H 0.79
S H 0.66
Q H 0.62
C H 0.62
A H 0.59
S H 0.52
M C 0.55
L C 0.66
N C 0.81
V C 0.79
A C 0.79
L C 0.75
R C 0.77
P C 0.72
E C 0.57
M E 0.67
Q E 0.83
L E 0.87
E E 0.88
Q E 0.84
V E 0.61
G C 0.86
G C 0.91
K E 0.51
T E 0.87
L E 0.93
L E 0.93
V E 0.93
V E 0.91
Y E 0.87
V E 0.60
P C 0.73
E C 0.82
A C 0.84
D C 0.86
V C 0.66
T C 0.74
H C 0.75
K C 0.74
P C 0.64
I E 0.77
Y E 0.85
K E 0.77
K E 0.58
A C 0.65
T C 0.80
G C 0.80
L C 0.74
P C 0.70
G C 0.77
G C 0.68
A E 0.63
Y E 0.84
R E 0.84
R E 0.75
I C 0.48
G C 0.83
S C 0.87
S C 0.82
D C 0.76
Q C 0.64
R C 0.60
C C 0.78
V C 0.92
END