PFRMAT SS
TARGET YEL009C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YEL009C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YEL009C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YEL009C.t2k.str2.rdb  (weight 1.54758)
METHOD YEL009C.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 YEL009C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YEL009C
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 YEL009C.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 323
METHOD
METHOD ============================================
METHOD Comments from YEL009C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YEL009C
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 YEL009C.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 323
METHOD
METHOD ============================================
METHOD Comments from YEL009C.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YEL009C
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 YEL009C.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 323
METHOD
METHOD ============================================
METHOD Comments from YEL009C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YEL009C
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 YEL009C.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 323
METHOD
METHOD ============================================
MODEL 1
M C 0.83
S C 0.76
E C 0.77
Y C 0.67
Q C 0.59
P C 0.56
S C 0.59
L C 0.61
F C 0.65
A C 0.73
L C 0.68
N C 0.66
P C 0.54
M C 0.57
G C 0.61
F C 0.66
S C 0.67
P C 0.62
L C 0.66
D C 0.65
G C 0.68
S C 0.67
K C 0.67
S C 0.69
T C 0.71
N C 0.76
E C 0.71
N C 0.73
V C 0.69
S C 0.68
A C 0.66
S C 0.66
T C 0.72
S C 0.74
T C 0.69
A C 0.71
K C 0.67
P C 0.64
M C 0.69
V C 0.70
G C 0.54
Q H 0.60
L H 0.62
I H 0.54
F C 0.52
D C 0.56
K C 0.54
F C 0.50
I C 0.52
K C 0.52
T C 0.53
E C 0.55
E C 0.63
D C 0.70
P C 0.75
I C 0.77
I C 0.73
K C 0.77
Q C 0.71
D C 0.67
T C 0.76
P C 0.61
S C 0.55
N C 0.51
L C 0.53
D C 0.57
F C 0.50
D C 0.50
F C 0.54
A C 0.62
L C 0.72
P C 0.73
Q C 0.65
T C 0.60
A C 0.63
T C 0.68
A C 0.74
P C 0.72
D C 0.72
A C 0.69
K C 0.67
T C 0.62
V C 0.63
L C 0.67
P C 0.64
I C 0.66
P C 0.56
E C 0.50
L C 0.50
D C 0.55
D C 0.62
A C 0.65
V C 0.68
V C 0.69
E C 0.70
S C 0.73
F C 0.68
F C 0.65
S C 0.65
S C 0.64
S C 0.62
T C 0.64
D C 0.68
S C 0.68
T C 0.68
P C 0.65
M C 0.64
F C 0.64
E C 0.68
Y C 0.70
E C 0.70
N C 0.73
L C 0.70
E C 0.73
D C 0.71
N C 0.74
S C 0.63
K C 0.56
E C 0.53
W C 0.53
T C 0.56
S C 0.61
L C 0.65
F C 0.72
D C 0.74
N C 0.73
D C 0.73
I C 0.75
P C 0.73
V C 0.68
T C 0.67
T C 0.65
D C 0.65
D C 0.60
V C 0.60
S C 0.63
L C 0.62
A C 0.66
D C 0.67
K C 0.68
A C 0.66
I C 0.66
E C 0.66
S C 0.61
T C 0.60
E C 0.60
E C 0.60
V C 0.62
S C 0.64
L C 0.64
V C 0.68
P C 0.69
S C 0.70
N C 0.73
L C 0.76
E C 0.74
V C 0.75
S C 0.77
T C 0.75
T C 0.73
S C 0.75
F C 0.74
L C 0.76
P C 0.74
T C 0.76
P C 0.73
V C 0.70
L C 0.73
E C 0.75
D C 0.71
A C 0.72
K C 0.71
L C 0.74
T C 0.74
Q C 0.74
T C 0.70
R C 0.71
K C 0.73
V C 0.72
K C 0.72
K C 0.77
P C 0.75
N C 0.75
S C 0.72
V C 0.72
V C 0.71
K C 0.73
K C 0.75
S C 0.74
H C 0.71
H C 0.71
V C 0.73
G C 0.76
K C 0.74
D C 0.73
D C 0.70
E C 0.65
S C 0.64
R C 0.65
L C 0.69
D C 0.70
H C 0.68
L C 0.67
G C 0.67
V C 0.67
V C 0.66
A C 0.67
Y C 0.65
N C 0.67
R C 0.64
K C 0.66
Q C 0.69
R C 0.70
S C 0.72
I C 0.75
P C 0.76
L C 0.75
S C 0.79
P C 0.71
I C 0.69
V C 0.71
P C 0.67
E H 0.52
S H 0.61
S H 0.66
D H 0.83
P H 0.89
A H 0.92
A H 0.94
L H 0.94
K H 0.94
R H 0.94
A H 0.93
R H 0.91
N H 0.87
T H 0.89
E H 0.92
A H 0.93
A H 0.93
R H 0.93
R H 0.91
S H 0.90
R H 0.92
A H 0.94
R H 0.94
K H 0.95
L H 0.95
Q H 0.95
R H 0.95
M H 0.95
K H 0.95
Q H 0.95
L H 0.96
E H 0.96
D H 0.96
K H 0.96
V H 0.96
E H 0.96
E H 0.96
L H 0.96
L H 0.95
S H 0.95
K H 0.93
N H 0.93
Y H 0.94
H H 0.94
L H 0.95
E H 0.96
N H 0.96
E H 0.96
V H 0.96
A H 0.96
R H 0.95
L H 0.95
K H 0.95
K H 0.93
L H 0.90
V H 0.84
G H 0.58
E C 0.55
R C 0.84
END