PFRMAT SS
TARGET YGR206W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR206W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR206W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR206W.t2k.str.rdb  (weight 1.53983)
METHOD YGR206W.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 YGR206W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR206W
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 YGR206W.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 1
METHOD
METHOD ============================================
METHOD Comments from YGR206W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR206W
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 YGR206W.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 1
METHOD
METHOD ============================================
METHOD Comments from YGR206W.t2k.str.rdb
METHOD ============================================
METHOD TARGET YGR206W
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 YGR206W.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 1
METHOD
METHOD ============================================
METHOD Comments from YGR206W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR206W
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 YGR206W.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 1
METHOD
METHOD ============================================
MODEL 1
M C 0.90
N C 0.77
N C 0.67
N C 0.52
V H 0.80
E H 0.86
E H 0.87
L H 0.88
L H 0.85
R H 0.78
R H 0.66
I C 0.54
P C 0.58
L C 0.44
Y C 0.45
N C 0.49
K C 0.53
Y C 0.65
G C 0.74
K C 0.72
D C 0.71
F C 0.78
P C 0.77
Q C 0.56
E C 0.49
T C 0.42
V E 0.39
T E 0.38
R E 0.38
F C 0.46
Q C 0.57
M C 0.71
P C 0.70
E C 0.59
F C 0.61
K C 0.66
L C 0.74
P C 0.71
A C 0.65
L C 0.68
Q C 0.76
P C 0.70
T C 0.62
R C 0.49
D C 0.48
L C 0.45
L C 0.52
C C 0.58
P H 0.55
W H 0.60
Y H 0.67
E H 0.64
E H 0.58
C H 0.52
D C 0.51
N C 0.57
I H 0.43
T H 0.44
K H 0.45
V H 0.42
C E 0.38
Q E 0.44
L C 0.45
H C 0.61
D C 0.69
S C 0.66
S C 0.65
N C 0.64
K C 0.49
K H 0.53
F H 0.62
D H 0.66
Q H 0.74
W H 0.76
Y H 0.74
K H 0.76
E H 0.75
Q H 0.70
Y H 0.61
L H 0.54
S C 0.56
K C 0.69
K C 0.83
P C 0.86
P C 0.76
G C 0.71
I C 0.55
V C 0.52
G C 0.60
N C 0.60
T C 0.50
L C 0.45
L C 0.56
S C 0.73
P C 0.65
S C 0.64
R C 0.59
K C 0.69
D C 0.75
N C 0.85
S C 0.92
END