PFRMAT SS
TARGET YGR207C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR207C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR207C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR207C.t2k.str2.rdb  (weight 1.54758)
METHOD YGR207C.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 YGR207C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR207C
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 YGR207C.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 124
METHOD
METHOD ============================================
METHOD Comments from YGR207C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR207C
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 YGR207C.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 124
METHOD
METHOD ============================================
METHOD Comments from YGR207C.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YGR207C
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 YGR207C.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 124
METHOD
METHOD ============================================
METHOD Comments from YGR207C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR207C
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 YGR207C.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 124
METHOD
METHOD ============================================
MODEL 1
M C 0.89
S C 0.80
A C 0.66
K C 0.69
Q C 0.68
Q C 0.51
L C 0.50
R E 0.66
I E 0.92
L E 0.92
V E 0.92
P E 0.91
V E 0.81
K E 0.71
R E 0.71
V E 0.55
V C 0.58
D C 0.81
F C 0.75
Q C 0.73
I C 0.63
K C 0.53
P E 0.75
R E 0.84
V E 0.84
N C 0.53
K C 0.84
T C 0.90
L C 0.88
T C 0.81
G E 0.63
I E 0.81
E E 0.69
T E 0.43
S C 0.68
G C 0.85
I C 0.79
K C 0.62
F E 0.53
S E 0.49
I C 0.66
N C 0.87
P H 0.80
F H 0.85
D H 0.91
D H 0.95
I H 0.95
A H 0.96
V H 0.96
E H 0.96
E H 0.96
A H 0.95
I H 0.94
R H 0.92
I H 0.90
K H 0.90
E H 0.86
K H 0.73
N C 0.61
K C 0.91
S C 0.90
L C 0.79
V C 0.64
E E 0.50
S E 0.78
T E 0.86
H E 0.91
A E 0.93
V E 0.92
S E 0.89
I E 0.60
G C 0.84
S C 0.77
A H 0.84
K H 0.87
A H 0.92
Q H 0.94
D H 0.95
I H 0.95
L H 0.95
R H 0.96
N H 0.96
C H 0.95
L H 0.94
A H 0.85
K C 0.62
G C 0.92
I C 0.90
D C 0.89
T E 0.81
C E 0.92
S E 0.92
L E 0.92
I E 0.72
D C 0.66
S C 0.83
V H 0.54
G H 0.60
K H 0.67
E C 0.61
N C 0.81
I C 0.85
E C 0.85
P H 0.90
L H 0.95
A H 0.96
I H 0.96
A H 0.96
K H 0.96
I H 0.96
L H 0.96
K H 0.96
A H 0.95
V H 0.95
V H 0.93
E H 0.89
K H 0.76
K H 0.51
G C 0.90
S C 0.89
N C 0.79
L E 0.92
V E 0.93
L E 0.93
M E 0.85
G C 0.52
K C 0.68
Q C 0.51
A C 0.51
I C 0.63
D C 0.76
D C 0.76
D C 0.76
C C 0.67
N C 0.62
N H 0.53
T H 0.66
G H 0.89
Q H 0.95
M H 0.96
L H 0.96
A H 0.96
G H 0.95
L H 0.92
L H 0.54
N C 0.92
W C 0.92
P C 0.80
Q C 0.44
A E 0.65
T E 0.65
N E 0.67
A E 0.65
A E 0.66
K E 0.74
V E 0.81
E E 0.81
F E 0.84
L E 0.65
D C 0.57
N C 0.91
G C 0.88
R E 0.81
V E 0.92
Q E 0.92
V E 0.92
T E 0.91
R E 0.88
E E 0.82
I E 0.54
D C 0.78
D C 0.88
G C 0.67
E E 0.70
E E 0.91
V E 0.91
I E 0.88
E E 0.80
A C 0.54
S C 0.79
L C 0.86
P C 0.69
M E 0.77
V E 0.91
I E 0.92
T E 0.89
T E 0.77
D C 0.50
L C 0.73
R C 0.78
L C 0.76
N C 0.81
T C 0.80
P C 0.77
R C 0.75
Y C 0.79
V C 0.79
G C 0.79
L H 0.81
P H 0.89
K H 0.88
L H 0.90
M H 0.84
K H 0.68
A H 0.58
K C 0.55
K C 0.70
K C 0.81
P C 0.79
I C 0.60
E E 0.49
K E 0.59
L C 0.52
D C 0.69
I H 0.70
A H 0.72
K H 0.78
D H 0.50
F C 0.72
P C 0.70
E C 0.73
I C 0.68
N C 0.73
I C 0.68
E C 0.69
P C 0.70
Q C 0.70
L C 0.56
K E 0.77
I E 0.88
V E 0.85
S E 0.84
M E 0.73
E C 0.51
E C 0.74
P C 0.87
K C 0.83
T C 0.75
K C 0.70
S C 0.72
P C 0.72
G C 0.65
V E 0.57
K E 0.70
L C 0.50
N C 0.82
S C 0.88
V H 0.88
D H 0.94
E H 0.95
L H 0.96
I H 0.96
E H 0.95
K H 0.95
L H 0.95
K H 0.92
E H 0.84
V H 0.54
K C 0.71
A C 0.84
I C 0.92
END