PFRMAT SS
TARGET YGR029W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR029W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR029W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR029W.t2k.str2.rdb  (weight 1.54758)
METHOD YGR029W.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 YGR029W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR029W
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 YGR029W.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 34
METHOD
METHOD ============================================
METHOD Comments from YGR029W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR029W
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 YGR029W.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 34
METHOD
METHOD ============================================
METHOD Comments from YGR029W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR029W
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 YGR029W.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 34
METHOD
METHOD ============================================
METHOD Comments from YGR029W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR029W
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 YGR029W.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 34
METHOD
METHOD ============================================
MODEL 1
M C 0.74
K C 0.60
A C 0.57
I C 0.60
D C 0.62
K C 0.67
M C 0.73
T C 0.81
D C 0.85
N C 0.87
P C 0.75
P C 0.59
Q C 0.50
E C 0.52
G C 0.65
L C 0.68
S C 0.71
G C 0.72
R C 0.74
K C 0.63
I E 0.55
I E 0.57
Y E 0.51
D C 0.77
E C 0.86
D C 0.90
G C 0.92
K C 0.89
P C 0.71
C C 0.73
R C 0.64
S C 0.62
C C 0.68
N C 0.71
T C 0.71
L C 0.52
L C 0.51
D H 0.46
F H 0.69
Q H 0.71
Y H 0.68
V H 0.51
T C 0.51
G C 0.55
K C 0.52
I C 0.56
S C 0.63
N C 0.75
G C 0.80
L C 0.77
K C 0.72
N C 0.70
L C 0.56
S C 0.47
S C 0.44
N C 0.44
G C 0.46
K C 0.43
L C 0.50
A C 0.61
G C 0.64
T C 0.70
G C 0.75
A C 0.64
L C 0.57
T C 0.52
G C 0.56
E C 0.49
A C 0.47
S H 0.46
E C 0.54
L C 0.61
M C 0.76
P C 0.73
G C 0.72
S C 0.72
R C 0.69
T C 0.66
Y C 0.66
R C 0.75
K C 0.76
V C 0.79
D C 0.85
P C 0.82
P C 0.79
D C 0.80
V H 0.63
E H 0.61
Q H 0.61
L H 0.50
G C 0.52
R H 0.85
S H 0.92
S H 0.94
W H 0.96
T H 0.96
L H 0.96
L H 0.95
H H 0.95
S H 0.94
V H 0.92
A H 0.88
A H 0.76
S H 0.52
Y C 0.74
P C 0.85
A C 0.87
Q C 0.90
P C 0.89
T C 0.89
D H 0.72
Q H 0.77
Q H 0.80
K H 0.90
G H 0.92
E H 0.93
M H 0.95
K H 0.95
Q H 0.95
F H 0.95
L H 0.95
N H 0.93
I H 0.89
F H 0.85
S H 0.74
H H 0.62
I H 0.50
Y C 0.74
P C 0.82
C C 0.64
N H 0.82
W H 0.89
C H 0.91
A H 0.94
K H 0.94
D H 0.93
F H 0.95
E H 0.96
K H 0.96
Y H 0.95
I H 0.94
R H 0.86
E H 0.71
N C 0.68
A C 0.83
P C 0.76
Q C 0.77
V C 0.80
E C 0.85
S C 0.85
R H 0.92
E H 0.94
E H 0.95
L H 0.96
G H 0.96
R H 0.96
W H 0.96
M H 0.96
C H 0.96
E H 0.94
A H 0.92
H H 0.87
N H 0.85
K H 0.85
V H 0.86
N H 0.84
K H 0.87
K H 0.81
L C 0.54
R C 0.90
K C 0.89
P C 0.77
K C 0.74
F C 0.77
D C 0.82
C H 0.51
N C 0.50
F C 0.48
W H 0.46
E H 0.46
K H 0.46
R H 0.48
W H 0.41
K C 0.42
D C 0.56
G C 0.69
W C 0.73
D C 0.78
E C 0.91
END