PFRMAT SS
TARGET YGR230W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR230W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR230W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR230W.t2k.str.rdb  (weight 1.53983)
METHOD YGR230W.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 YGR230W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR230W
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 YGR230W.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 4
METHOD
METHOD ============================================
METHOD Comments from YGR230W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR230W
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 YGR230W.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 4
METHOD
METHOD ============================================
METHOD Comments from YGR230W.t2k.str.rdb
METHOD ============================================
METHOD TARGET YGR230W
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.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 str )
METHOD The input amino acid frequencies were determined from
METHOD alignment YGR230W.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 4
METHOD
METHOD ============================================
METHOD Comments from YGR230W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR230W
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 YGR230W.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 4
METHOD
METHOD ============================================
MODEL 1
M C 0.91
S C 0.82
Y C 0.81
G C 0.83
G C 0.81
S C 0.69
A H 0.51
S H 0.61
Q H 0.83
D H 0.86
I H 0.92
V H 0.94
T H 0.95
K H 0.95
L H 0.95
I H 0.94
R H 0.91
K H 0.86
I H 0.76
Q H 0.54
N C 0.71
T C 0.74
S C 0.67
V C 0.51
S E 0.47
C E 0.48
T C 0.49
R C 0.53
R C 0.67
D C 0.67
E C 0.66
N C 0.73
L C 0.63
D C 0.56
S H 0.49
F H 0.61
N H 0.62
Q H 0.68
H H 0.61
L H 0.53
K H 0.42
M E 0.42
S E 0.47
L E 0.50
K E 0.51
V E 0.48
A C 0.38
H C 0.56
N C 0.68
T C 0.65
K H 0.47
T H 0.56
F H 0.73
A H 0.74
K H 0.73
H H 0.73
C H 0.71
L H 0.74
H H 0.79
R H 0.86
Q H 0.87
V H 0.86
F H 0.83
K H 0.79
N H 0.71
T H 0.59
Y H 0.52
R H 0.47
K H 0.54
R H 0.58
K H 0.52
A H 0.48
V C 0.51
E C 0.57
D C 0.69
Q H 0.52
R H 0.51
K H 0.53
N H 0.48
L H 0.58
N H 0.62
T H 0.67
Q H 0.69
L H 0.72
R H 0.69
Q H 0.59
K H 0.47
F C 0.67
A C 0.78
S C 0.86
P C 0.63
S C 0.67
D C 0.62
N C 0.59
L C 0.59
L C 0.60
S C 0.70
P C 0.54
C C 0.48
S H 0.61
R H 0.67
K H 0.60
L H 0.64
N H 0.66
D H 0.75
H H 0.71
K H 0.71
S H 0.68
K H 0.68
L H 0.62
F H 0.53
S C 0.47
A C 0.58
K C 0.66
S C 0.78
Q C 0.86
P C 0.83
K C 0.68
T C 0.53
L H 0.36
E H 0.37
F H 0.36
V C 0.42
R C 0.61
G C 0.75
K C 0.71
Q C 0.68
N C 0.72
I C 0.84
P C 0.85
R C 0.81
K C 0.84
P C 0.83
N C 0.83
V C 0.78
D C 0.85
I C 0.91
END