PFRMAT SS
TARGET YGR016W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR016W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR016W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR016W.t2k.str.rdb  (weight 1.53983)
METHOD YGR016W.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 YGR016W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR016W
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 YGR016W.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 YGR016W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR016W
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 YGR016W.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 YGR016W.t2k.str.rdb
METHOD ============================================
METHOD TARGET YGR016W
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 YGR016W.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 YGR016W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR016W
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 YGR016W.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 0.86
S C 0.62
R C 0.51
L H 0.50
R H 0.52
R H 0.54
F H 0.51
N C 0.44
R H 0.46
K H 0.44
I E 0.36
L E 0.40
S E 0.42
L C 0.46
S C 0.58
S C 0.62
D C 0.67
Y C 0.61
T C 0.64
H C 0.71
D C 0.80
G C 0.81
E C 0.73
S C 0.70
D C 0.69
Q C 0.60
E C 0.57
D C 0.55
V C 0.49
S E 0.52
I E 0.60
L E 0.50
P C 0.60
L C 0.73
D C 0.78
T C 0.51
E H 0.65
E H 0.70
Q H 0.80
E H 0.85
E H 0.86
L H 0.87
I H 0.87
Q H 0.85
K H 0.80
F H 0.69
E H 0.60
T H 0.49
N C 0.56
A C 0.51
H C 0.46
I H 0.43
T H 0.47
N H 0.59
K H 0.68
L H 0.68
Y H 0.70
I H 0.77
N H 0.79
L H 0.89
L H 0.91
S H 0.92
I H 0.94
L H 0.94
Y H 0.93
L H 0.90
L H 0.84
Y H 0.69
G C 0.52
G C 0.55
L E 0.38
L E 0.57
M E 0.70
I E 0.75
L E 0.76
V E 0.71
R E 0.58
K C 0.49
S C 0.59
R C 0.60
G C 0.56
Y H 0.39
I E 0.44
K E 0.44
L H 0.50
A H 0.52
L H 0.54
L H 0.48
A C 0.45
G C 0.66
A C 0.64
N C 0.64
S C 0.49
L E 0.46
I E 0.58
C E 0.55
S E 0.48
C E 0.53
I E 0.58
T E 0.60
L E 0.51
R E 0.42
Y H 0.41
D H 0.41
I H 0.50
V H 0.57
N H 0.57
D H 0.63
Y H 0.61
L H 0.54
L H 0.47
F H 0.47
K H 0.47
K H 0.40
F E 0.38
K E 0.51
L E 0.58
R E 0.57
V E 0.48
S C 0.54
N C 0.59
F C 0.48
S C 0.40
I H 0.51
N H 0.62
I H 0.86
I H 0.91
N H 0.93
I H 0.94
I H 0.95
L H 0.95
L H 0.94
V H 0.94
L H 0.94
M H 0.93
A H 0.90
W H 0.83
I H 0.72
S H 0.56
F H 0.52
N C 0.45
H C 0.42
V E 0.38
V E 0.42
E C 0.48
D C 0.62
K C 0.64
K C 0.57
T E 0.57
V E 0.72
L E 0.71
C E 0.68
L E 0.54
Q E 0.43
V C 0.48
P H 0.44
M H 0.65
F H 0.76
L H 0.82
F H 0.85
W H 0.87
V H 0.91
A H 0.92
V H 0.92
L H 0.90
V H 0.90
K H 0.90
R H 0.86
W H 0.84
A H 0.81
R H 0.74
N H 0.60
I H 0.72
E H 0.78
D H 0.78
E H 0.80
I H 0.81
A H 0.77
D H 0.70
L H 0.70
R H 0.69
C H 0.64
L H 0.60
K H 0.55
Y H 0.50
K H 0.46
Y C 0.48
K C 0.62
N C 0.80
A C 0.92
END