PFRMAT SS
TARGET T0178
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0178.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0178.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0178.t2k.str.rdb  (weight 1.53983)
METHOD T0178.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 T0178.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0178
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 T0178.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 52
METHOD
METHOD ============================================
METHOD Comments from T0178.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0178
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 T0178.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 52
METHOD
METHOD ============================================
METHOD Comments from T0178.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0178
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 T0178.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 52
METHOD
METHOD ============================================
METHOD Comments from T0178.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0178
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 T0178.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 52
METHOD
METHOD ============================================
MODEL 1
M C 0.74
I H 0.65
D H 0.70
V H 0.84
R H 0.87
K H 0.87
Y H 0.85
I H 0.79
D H 0.73
N H 0.69
A H 0.51
A C 0.67
L C 0.80
K C 0.88
P C 0.77
H C 0.85
L C 0.87
S C 0.91
E H 0.92
K H 0.95
E H 0.95
I H 0.96
E H 0.96
E H 0.96
F H 0.96
V H 0.96
L H 0.95
K H 0.94
S H 0.93
E H 0.88
E H 0.73
L C 0.65
G C 0.92
I C 0.82
Y E 0.60
A E 0.88
V E 0.91
C E 0.89
V E 0.68
N C 0.78
P C 0.56
Y H 0.59
H H 0.70
V H 0.85
K H 0.94
L H 0.94
A H 0.95
S H 0.94
S H 0.91
I H 0.80
A H 0.56
K C 0.62
K C 0.85
V C 0.75
K E 0.56
V E 0.89
C E 0.87
C E 0.83
V E 0.77
I C 0.49
G C 0.74
F C 0.80
P C 0.80
L C 0.83
G C 0.87
L C 0.82
N C 0.76
K C 0.46
T H 0.78
S H 0.89
V H 0.91
K H 0.94
V H 0.95
K H 0.96
E H 0.96
A H 0.95
V H 0.96
E H 0.95
A H 0.94
V H 0.92
R H 0.83
D C 0.63
G C 0.85
A C 0.84
Q C 0.69
E E 0.55
L E 0.68
D E 0.72
I E 0.83
V E 0.74
W E 0.60
N C 0.61
L H 0.68
S H 0.78
A H 0.83
F H 0.81
K H 0.67
S C 0.58
E C 0.85
K C 0.71
Y H 0.88
D H 0.93
F H 0.94
V H 0.95
V H 0.96
E H 0.96
E H 0.96
L H 0.96
K H 0.96
E H 0.96
I H 0.96
F H 0.95
R H 0.93
E H 0.85
T H 0.49
P C 0.80
S C 0.89
A C 0.74
V E 0.62
H E 0.86
K E 0.89
V E 0.90
I E 0.87
V E 0.78
E E 0.60
T C 0.50
P C 0.58
Y C 0.61
L C 0.80
N C 0.90
E H 0.92
E H 0.95
E H 0.95
I H 0.96
K H 0.96
K H 0.96
A H 0.96
V H 0.96
E H 0.96
I H 0.96
C H 0.96
I H 0.95
E H 0.92
A H 0.51
G C 0.90
A C 0.89
D C 0.77
F E 0.63
I E 0.70
K E 0.67
T C 0.55
S C 0.75
T C 0.81
G C 0.85
F C 0.80
A C 0.79
P C 0.82
R C 0.86
G C 0.90
T C 0.88
T C 0.84
L H 0.94
E H 0.95
E H 0.96
V H 0.96
R H 0.96
L H 0.96
I H 0.96
K H 0.96
S H 0.95
S H 0.90
A H 0.71
K H 0.49
G C 0.60
R C 0.70
I C 0.74
K C 0.72
V E 0.55
K E 0.61
A C 0.47
S C 0.69
G C 0.81
G C 0.78
I C 0.68
R C 0.74
D C 0.86
L H 0.93
E H 0.95
T H 0.95
A H 0.96
I H 0.96
S H 0.96
M H 0.96
I H 0.95
E H 0.94
A H 0.88
G H 0.82
A H 0.81
D H 0.82
R H 0.77
I H 0.61
G C 0.53
T H 0.47
S H 0.59
S H 0.74
G H 0.86
I H 0.93
S H 0.94
I H 0.94
A H 0.91
E H 0.81
E H 0.60
F C 0.53
L C 0.64
K C 0.74
R C 0.75
H C 0.73
L C 0.80
I C 0.92
END