PFRMAT SS
TARGET YDL134C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YDL134C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YDL134C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YDL134C.t2k.str2.rdb  (weight 1.54758)
METHOD YDL134C.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 YDL134C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YDL134C
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 YDL134C.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 270
METHOD
METHOD ============================================
METHOD Comments from YDL134C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YDL134C
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 YDL134C.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 270
METHOD
METHOD ============================================
METHOD Comments from YDL134C.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YDL134C
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 YDL134C.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 270
METHOD
METHOD ============================================
METHOD Comments from YDL134C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YDL134C
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 YDL134C.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 270
METHOD
METHOD ============================================
MODEL 1
M C 0.85
D C 0.65
T C 0.52
D C 0.59
L C 0.75
D C 0.77
V C 0.79
P C 0.76
M C 0.51
Q H 0.50
D H 0.60
A H 0.66
V H 0.65
T H 0.63
E H 0.81
Q H 0.88
L H 0.91
T H 0.92
P H 0.93
T H 0.92
V H 0.91
S H 0.89
E H 0.87
D H 0.84
M H 0.86
D H 0.87
L H 0.85
N H 0.80
N H 0.74
N H 0.62
S H 0.58
S H 0.51
D C 0.53
N C 0.60
N C 0.62
A C 0.56
E C 0.47
E C 0.38
F E 0.35
S E 0.40
V E 0.41
D C 0.47
D C 0.59
L C 0.65
K C 0.71
P C 0.58
G C 0.55
S C 0.53
S C 0.63
G C 0.70
I C 0.63
A C 0.62
D C 0.58
H C 0.62
K C 0.68
S C 0.73
S C 0.76
K C 0.70
P C 0.55
L C 0.51
E C 0.52
L C 0.57
N C 0.60
N C 0.52
T C 0.51
N C 0.47
I H 0.70
N H 0.77
Q H 0.84
L H 0.90
D H 0.91
Q H 0.91
W H 0.88
I H 0.85
E H 0.80
H H 0.72
L H 0.57
S H 0.51
K C 0.56
C C 0.72
E C 0.72
P C 0.69
L C 0.81
S C 0.90
E H 0.93
D H 0.94
D H 0.95
V H 0.96
A H 0.96
R H 0.96
L H 0.96
C H 0.96
K H 0.96
M H 0.95
A H 0.95
V H 0.95
D H 0.95
V H 0.93
L H 0.89
Q H 0.75
F C 0.50
E C 0.82
E C 0.81
N C 0.71
V C 0.58
K E 0.54
P C 0.50
I C 0.65
N C 0.86
V C 0.88
P C 0.72
V E 0.79
T E 0.90
I E 0.90
C E 0.74
G E 0.49
D C 0.67
V C 0.62
H C 0.61
G C 0.66
Q C 0.60
F H 0.86
H H 0.93
D H 0.95
L H 0.95
L H 0.96
E H 0.96
L H 0.95
F H 0.95
K H 0.92
I H 0.82
G C 0.52
G C 0.89
P C 0.89
C C 0.89
P C 0.80
D C 0.82
T C 0.78
N E 0.52
Y E 0.89
L E 0.91
F E 0.89
M E 0.73
G E 0.48
D C 0.59
Y C 0.50
V C 0.52
D C 0.64
R C 0.76
G C 0.81
Y C 0.68
Y C 0.62
S H 0.62
V H 0.95
E H 0.96
T H 0.96
V H 0.96
S H 0.96
Y H 0.96
L H 0.95
V H 0.93
A H 0.86
M H 0.70
K H 0.55
V H 0.47
R C 0.49
Y C 0.75
P C 0.85
H C 0.88
R C 0.57
I E 0.86
T E 0.91
I E 0.91
L E 0.80
R C 0.52
G C 0.78
N C 0.55
H H 0.54
E H 0.75
S H 0.79
R H 0.80
Q H 0.82
I H 0.86
T H 0.86
Q H 0.84
V H 0.78
Y H 0.61
G C 0.65
F C 0.57
Y H 0.67
D H 0.81
E H 0.83
C H 0.83
L H 0.79
R H 0.73
K H 0.63
Y C 0.59
G C 0.75
S C 0.71
A H 0.66
N H 0.76
V H 0.87
W H 0.94
K H 0.95
M H 0.95
F H 0.95
T H 0.95
D H 0.94
L H 0.91
F H 0.89
D H 0.76
Y H 0.53
F C 0.74
P C 0.64
I E 0.50
T E 0.73
A E 0.83
L E 0.84
V E 0.72
D C 0.86
N C 0.90
K E 0.66
I E 0.92
F E 0.93
C E 0.92
L E 0.87
H E 0.64
G C 0.72
G C 0.80
L C 0.78
S C 0.85
P C 0.71
M C 0.73
I C 0.72
E C 0.81
T C 0.86
I H 0.85
D H 0.86
Q H 0.86
V H 0.84
R H 0.75
E H 0.57
L C 0.55
N C 0.61
R C 0.69
I C 0.74
Q C 0.68
E C 0.68
V C 0.82
P C 0.84
H C 0.81
E C 0.81
G C 0.79
P C 0.59
M C 0.43
C H 0.43
D H 0.43
L H 0.42
L C 0.36
W C 0.51
S C 0.69
D C 0.82
P C 0.70
D C 0.70
D C 0.70
R C 0.75
G C 0.77
G C 0.79
W C 0.70
G C 0.65
I C 0.66
S C 0.83
P C 0.79
R C 0.86
G C 0.84
A C 0.73
G C 0.48
F E 0.60
T E 0.56
F C 0.55
G C 0.78
Q H 0.68
D H 0.88
V H 0.94
S H 0.95
E H 0.96
Q H 0.96
F H 0.96
N H 0.95
H H 0.94
T H 0.86
N C 0.55
D C 0.91
L C 0.83
S C 0.54
L E 0.74
I E 0.83
A E 0.84
R E 0.65
A C 0.40
H C 0.48
Q E 0.40
L E 0.41
V C 0.48
M C 0.56
E C 0.72
G C 0.64
Y E 0.60
A E 0.83
W E 0.83
S E 0.73
H E 0.46
Q C 0.87
Q C 0.89
N E 0.54
V E 0.89
V E 0.91
T E 0.92
I E 0.87
F E 0.77
S E 0.55
A C 0.76
P C 0.72
N C 0.68
Y C 0.56
C C 0.56
Y C 0.65
R C 0.62
C C 0.73
G C 0.81
N C 0.74
Q E 0.61
A E 0.82
A E 0.88
I E 0.91
M E 0.91
E E 0.90
V E 0.83
D C 0.66
E C 0.86
N C 0.90
H C 0.79
N C 0.61
R E 0.65
Q E 0.72
F E 0.87
L E 0.89
Q E 0.89
Y E 0.79
D E 0.59
P C 0.57
S C 0.76
V C 0.85
R C 0.88
P C 0.81
G C 0.81
E C 0.78
P C 0.74
S C 0.71
V C 0.70
S C 0.75
R C 0.73
K C 0.68
T C 0.74
P C 0.72
D C 0.61
Y C 0.59
F C 0.66
L C 0.88
END