PFRMAT SS
TARGET YGR008C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR008C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR008C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR008C.t2k.str.rdb  (weight 1.53983)
METHOD YGR008C.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 YGR008C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR008C
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 YGR008C.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 2
METHOD
METHOD ============================================
METHOD Comments from YGR008C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR008C
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 YGR008C.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 2
METHOD
METHOD ============================================
METHOD Comments from YGR008C.t2k.str.rdb
METHOD ============================================
METHOD TARGET YGR008C
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 YGR008C.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 2
METHOD
METHOD ============================================
METHOD Comments from YGR008C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR008C
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 YGR008C.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 2
METHOD
METHOD ============================================
MODEL 1
M C 0.91
T C 0.75
R C 0.71
T C 0.75
N C 0.74
K C 0.63
W C 0.57
T C 0.52
E C 0.41
R C 0.46
E C 0.48
G C 0.55
K C 0.60
A C 0.70
D C 0.85
P C 0.73
K C 0.63
Y C 0.48
F E 0.51
S C 0.51
H C 0.65
T C 0.81
G C 0.86
N C 0.79
Y C 0.77
G C 0.80
E C 0.77
S C 0.83
P C 0.64
N C 0.60
H C 0.46
I C 0.41
K C 0.47
K C 0.55
Q C 0.77
G C 0.80
S C 0.78
G C 0.78
K C 0.78
G C 0.81
N C 0.79
W C 0.81
G C 0.84
K C 0.84
P C 0.79
G C 0.80
D C 0.64
E C 0.43
I H 0.51
D H 0.53
D H 0.51
L H 0.50
I H 0.41
D C 0.57
N C 0.75
G C 0.81
E C 0.68
I C 0.59
P C 0.69
P C 0.56
V C 0.47
F C 0.45
K C 0.55
K C 0.60
D C 0.66
R C 0.69
R C 0.76
G C 0.80
S C 0.79
N C 0.76
L C 0.64
Q C 0.55
S H 0.47
H H 0.56
E H 0.72
Q H 0.70
K H 0.68
F H 0.73
E H 0.72
N H 0.65
V H 0.55
Q C 0.49
K C 0.66
E C 0.91
END