PFRMAT SS
TARGET T0134
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0134.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0134.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0134.t2k.str.rdb  (weight 1.53983)
METHOD T0134.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 T0134.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0134
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 T0134.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 4
METHOD
METHOD ============================================
METHOD Comments from T0134.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0134
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 T0134.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 4
METHOD
METHOD ============================================
METHOD Comments from T0134.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0134
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 T0134.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 4
METHOD
METHOD ============================================
METHOD Comments from T0134.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0134
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 T0134.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 4
METHOD
METHOD ============================================
MODEL 1
G C 0.92
E C 0.84
P C 0.74
V C 0.68
Q C 0.68
N C 0.64
G C 0.69
A C 0.71
P C 0.63
E C 0.65
E C 0.73
E C 0.79
Q C 0.82
L C 0.86
P C 0.89
P C 0.79
E C 0.79
S C 0.75
S H 0.51
Y H 0.59
S H 0.62
L H 0.62
L H 0.55
A H 0.44
E C 0.55
N C 0.73
S C 0.71
Y E 0.48
V E 0.70
K E 0.81
M E 0.88
T E 0.85
C E 0.79
D E 0.53
I C 0.68
R C 0.79
G C 0.76
S C 0.81
L C 0.58
Q C 0.59
E C 0.62
D C 0.81
S C 0.79
Q E 0.50
V E 0.81
T E 0.89
V E 0.91
A E 0.92
I E 0.92
V E 0.92
L E 0.86
E E 0.60
N C 0.65
R C 0.74
S C 0.77
S C 0.57
S C 0.48
I H 0.41
L C 0.35
K E 0.34
G E 0.43
M E 0.45
E E 0.50
L E 0.39
S H 0.38
V H 0.57
L H 0.61
D H 0.61
S H 0.59
L H 0.58
N H 0.51
A H 0.49
R H 0.48
M H 0.37
A C 0.45
R C 0.75
P C 0.82
Q C 0.86
G C 0.87
S C 0.83
S C 0.69
V C 0.70
H C 0.74
D C 0.79
G C 0.79
V C 0.60
P C 0.54
V C 0.64
P C 0.63
F C 0.60
Q C 0.66
L C 0.81
P C 0.90
P C 0.83
G C 0.88
V C 0.81
S C 0.83
N C 0.77
E C 0.67
A C 0.55
Q E 0.59
Y E 0.80
V E 0.87
F E 0.85
T E 0.85
I E 0.78
Q E 0.68
S E 0.55
I H 0.47
V H 0.59
M H 0.70
A H 0.72
Q H 0.63
K H 0.53
L C 0.47
K C 0.60
G C 0.49
T E 0.68
L E 0.79
S E 0.83
F E 0.83
I E 0.83
A E 0.69
K C 0.50
N C 0.70
D C 0.78
E C 0.81
G C 0.84
A C 0.81
T C 0.76
H C 0.65
E C 0.52
K C 0.45
L E 0.43
D E 0.46
F E 0.59
R E 0.59
L E 0.48
H C 0.52
F C 0.54
S C 0.54
C E 0.56
S E 0.60
S E 0.76
Y E 0.84
L E 0.84
I E 0.64
T C 0.67
T C 0.82
P C 0.81
C C 0.78
Y C 0.74
S C 0.61
D H 0.60
A H 0.81
F H 0.87
A H 0.90
K H 0.89
L H 0.88
L H 0.80
E H 0.59
S C 0.66
G C 0.86
D C 0.80
L C 0.58
S C 0.62
M C 0.58
S C 0.65
S C 0.53
I E 0.66
K E 0.75
V E 0.65
D C 0.66
G C 0.64
I E 0.63
R E 0.74
M E 0.77
S E 0.72
F H 0.68
Q H 0.87
N H 0.88
L H 0.93
L H 0.93
A H 0.94
K H 0.93
I H 0.91
C H 0.87
F H 0.77
H H 0.58
H C 0.60
H C 0.73
F C 0.55
S E 0.60
V E 0.70
V E 0.72
E E 0.67
R E 0.54
V C 0.57
D C 0.66
S C 0.48
C H 0.52
A H 0.43
S C 0.40
M H 0.44
Y C 0.44
S C 0.50
R C 0.43
S C 0.50
I C 0.68
Q C 0.87
G C 0.88
H C 0.68
H E 0.69
V E 0.84
C E 0.89
L E 0.90
L E 0.90
V E 0.87
K E 0.81
K E 0.56
G C 0.73
E C 0.80
N C 0.83
S C 0.61
V E 0.71
S E 0.79
V E 0.71
D C 0.68
G C 0.82
K C 0.75
C C 0.76
S C 0.86
D C 0.79
S H 0.81
T H 0.87
L H 0.91
L H 0.94
S H 0.94
N H 0.94
L H 0.94
L H 0.95
E H 0.95
E H 0.92
M H 0.93
K H 0.94
A H 0.93
T H 0.91
L H 0.84
A H 0.68
K C 0.53
C C 0.91
END