PFRMAT SS
TARGET YGR018C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR018C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR018C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR018C.t2k.str.rdb  (weight 1.53983)
METHOD YGR018C.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 YGR018C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR018C
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 YGR018C.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 YGR018C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR018C
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 YGR018C.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 YGR018C.t2k.str.rdb
METHOD ============================================
METHOD TARGET YGR018C
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 YGR018C.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 YGR018C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR018C
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 YGR018C.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 0.89
I C 0.70
D C 0.61
I C 0.63
S C 0.67
H C 0.71
G C 0.78
H C 0.69
T C 0.61
S C 0.61
C C 0.62
S C 0.63
S C 0.63
H C 0.64
R C 0.65
S C 0.63
S C 0.64
S C 0.67
L C 0.70
P C 0.61
S C 0.45
V E 0.38
F E 0.53
W E 0.56
K E 0.59
I E 0.57
H E 0.47
L C 0.60
S C 0.80
P C 0.83
P C 0.82
L C 0.78
P C 0.73
S C 0.63
F C 0.53
K C 0.46
F C 0.47
K C 0.54
K C 0.60
S C 0.66
T C 0.65
E C 0.58
S C 0.54
T C 0.52
Q C 0.51
R C 0.47
Q C 0.50
T C 0.53
I C 0.64
P C 0.69
K C 0.63
F C 0.66
S C 0.74
S C 0.77
P C 0.67
A C 0.52
S C 0.50
S C 0.55
L C 0.64
A C 0.77
P C 0.76
S C 0.77
T C 0.79
P C 0.68
L C 0.51
W C 0.45
S C 0.46
L C 0.42
S C 0.46
S C 0.43
C E 0.51
L E 0.65
L E 0.72
V E 0.67
S E 0.58
E E 0.54
V E 0.59
S E 0.58
F E 0.51
W C 0.59
P C 0.73
G C 0.77
A C 0.68
G C 0.60
F E 0.43
L E 0.49
Y E 0.41
N C 0.50
D C 0.47
L E 0.51
V E 0.64
C E 0.62
L E 0.46
D C 0.62
R C 0.58
E C 0.53
D C 0.49
H C 0.51
C C 0.50
L C 0.52
S C 0.58
N C 0.63
S C 0.62
A C 0.56
S C 0.56
H C 0.59
S C 0.67
C C 0.77
G C 0.93
END