PFRMAT SS
TARGET T0129
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0129.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0129.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0129.t2k.str.rdb  (weight 1.53983)
METHOD T0129.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 T0129.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0129
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 T0129.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 6
METHOD
METHOD ============================================
METHOD Comments from T0129.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0129
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 T0129.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 6
METHOD
METHOD ============================================
METHOD Comments from T0129.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0129
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 T0129.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 6
METHOD
METHOD ============================================
METHOD Comments from T0129.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0129
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 T0129.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 6
METHOD
METHOD ============================================
MODEL 1
M C 0.90
L C 0.76
I C 0.66
S C 0.62
H H 0.49
S H 0.79
D H 0.86
L H 0.91
N H 0.92
Q H 0.91
Q H 0.91
L H 0.88
K H 0.84
S H 0.76
A H 0.57
G C 0.74
I C 0.78
G C 0.80
F C 0.86
N C 0.87
A H 0.91
T H 0.93
E H 0.93
L H 0.92
H H 0.87
G H 0.80
F H 0.81
L H 0.76
S H 0.68
G C 0.46
L H 0.39
L C 0.37
C C 0.55
G C 0.78
G C 0.86
L C 0.79
K C 0.80
D C 0.54
Q H 0.64
S H 0.75
W H 0.90
L H 0.92
P H 0.94
L H 0.94
L H 0.94
Y H 0.93
Q H 0.90
F H 0.80
S H 0.50
N C 0.66
D C 0.74
N C 0.80
H C 0.78
A C 0.72
Y C 0.73
P H 0.60
T H 0.81
G H 0.84
L H 0.87
V H 0.88
Q H 0.89
P H 0.91
V H 0.94
T H 0.95
E H 0.94
L H 0.95
Y H 0.95
E H 0.94
Q H 0.93
I H 0.92
S H 0.91
Q H 0.88
T H 0.83
L H 0.69
S H 0.55
D C 0.62
V C 0.77
E C 0.84
G C 0.68
F E 0.69
T E 0.88
F E 0.91
E E 0.91
L E 0.88
G E 0.79
L C 0.55
T C 0.80
E C 0.87
D C 0.91
E C 0.82
N C 0.73
V H 0.49
F H 0.61
T H 0.65
Q H 0.79
A H 0.87
D H 0.90
S H 0.91
L H 0.95
S H 0.95
D H 0.95
W H 0.95
A H 0.95
N H 0.93
Q H 0.92
F H 0.90
L H 0.85
L H 0.77
G H 0.62
I C 0.47
G C 0.62
L C 0.58
A C 0.64
Q C 0.57
P H 0.51
E H 0.50
L H 0.58
A H 0.50
K C 0.49
E C 0.47
K C 0.48
G H 0.47
E H 0.61
I H 0.88
G H 0.91
E H 0.92
A H 0.93
V H 0.94
D H 0.94
D H 0.91
L H 0.94
Q H 0.95
D H 0.94
I H 0.93
C H 0.89
Q H 0.79
L H 0.50
G C 0.83
Y C 0.87
D C 0.85
E H 0.53
D C 0.50
D C 0.51
N C 0.65
E H 0.85
E H 0.88
E H 0.89
L H 0.91
A H 0.92
E H 0.92
A H 0.92
L H 0.94
E H 0.95
E H 0.95
I H 0.96
I H 0.96
E H 0.96
Y H 0.96
V H 0.96
R H 0.96
T H 0.96
I H 0.96
A H 0.96
M H 0.96
L H 0.95
F H 0.92
Y H 0.85
S H 0.74
H H 0.58
F C 0.65
N C 0.85
E C 0.89
G C 0.88
E C 0.86
I C 0.85
E C 0.85
S C 0.83
K C 0.87
P C 0.84
V C 0.76
L C 0.80
H C 0.92
END