PFRMAT SS
TARGET T0194
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0194.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0194.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0194.t2k.str.rdb  (weight 1.53983)
METHOD T0194.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 T0194.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0194
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 T0194.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 43
METHOD
METHOD ============================================
METHOD Comments from T0194.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0194
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 T0194.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 43
METHOD
METHOD ============================================
METHOD Comments from T0194.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0194
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 T0194.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 43
METHOD
METHOD ============================================
METHOD Comments from T0194.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0194
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 T0194.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 43
METHOD
METHOD ============================================
MODEL 1
M C 0.59
A H 0.51
N H 0.55
A H 0.54
P H 0.58
K C 0.54
G C 0.82
V C 0.83
K C 0.81
F C 0.82
S C 0.78
T C 0.75
S C 0.81
Q C 0.86
T C 0.86
T C 0.88
E H 0.86
E H 0.93
I H 0.95
V H 0.96
R H 0.96
A H 0.96
K H 0.95
V H 0.95
S H 0.95
E H 0.93
L H 0.90
V H 0.82
E H 0.52
Q C 0.77
Y C 0.88
D C 0.87
L E 0.83
I E 0.93
I E 0.93
G E 0.93
I E 0.91
P E 0.81
I E 0.51
D C 0.68
K C 0.60
E C 0.62
I C 0.54
S C 0.48
A H 0.69
S H 0.86
Y H 0.93
A H 0.94
N H 0.94
W H 0.96
K H 0.95
L H 0.94
V H 0.93
E H 0.91
K H 0.84
D H 0.69
Y C 0.55
A C 0.80
S C 0.84
K C 0.67
F E 0.79
H E 0.91
V E 0.90
L E 0.82
D E 0.50
A C 0.70
R C 0.61
A H 0.56
V H 0.63
E H 0.64
M H 0.77
I H 0.85
I H 0.92
D H 0.94
W H 0.95
L H 0.96
I H 0.96
N H 0.96
D H 0.96
I H 0.96
K H 0.96
G H 0.96
W H 0.95
L H 0.94
N H 0.88
T C 0.63
N C 0.92
P C 0.87
Y C 0.85
S C 0.87
R H 0.90
E H 0.94
G H 0.95
L H 0.96
D H 0.96
R H 0.96
F H 0.95
V H 0.95
E H 0.95
Q H 0.91
Y H 0.87
R H 0.77
K H 0.54
K C 0.72
T C 0.73
A C 0.49
A E 0.88
V E 0.92
L E 0.92
F E 0.89
V E 0.72
T C 0.58
D C 0.68
T H 0.54
K H 0.72
P H 0.73
L H 0.71
V H 0.59
A C 0.51
G C 0.74
G C 0.73
R C 0.63
L C 0.58
S C 0.56
N H 0.66
L H 0.82
K H 0.87
S H 0.83
F H 0.85
I H 0.89
I H 0.88
K H 0.84
S H 0.80
L C 0.47
K C 0.62
F C 0.56
H H 0.39
L H 0.46
L H 0.45
I H 0.45
S H 0.42
F E 0.38
L E 0.46
G C 0.84
E C 0.84
N C 0.91
G C 0.87
K C 0.60
L E 0.79
Q E 0.67
F E 0.53
F H 0.42
D H 0.45
K H 0.55
A H 0.46
R H 0.50
S C 0.55
A H 0.72
H H 0.91
D H 0.93
A H 0.95
H H 0.96
K H 0.96
L H 0.96
A H 0.96
V H 0.96
K H 0.96
F H 0.95
L H 0.95
K H 0.94
K H 0.88
Q H 0.79
L H 0.65
L H 0.54
K C 0.53
H C 0.66
S C 0.74
A C 0.76
K C 0.82
L C 0.73
K C 0.51
R E 0.60
G E 0.79
A E 0.89
F E 0.91
L E 0.91
T E 0.89
T E 0.78
V C 0.53
F C 0.78
D C 0.83
E C 0.49
Q H 0.77
T H 0.82
N H 0.89
T H 0.93
N H 0.93
L H 0.94
V H 0.95
Q H 0.95
E H 0.95
F H 0.94
D H 0.91
K H 0.80
L H 0.60
L C 0.61
D C 0.76
H C 0.75
S C 0.68
I C 0.56
N E 0.47
I E 0.57
E E 0.65
Q E 0.71
S E 0.68
L E 0.59
L C 0.52
S C 0.64
P C 0.47
V E 0.56
I E 0.61
C E 0.71
T E 0.66
H E 0.61
T C 0.44
G C 0.81
L C 0.87
N C 0.90
S C 0.50
Y E 0.84
V E 0.92
I E 0.92
V E 0.91
L E 0.86
Q E 0.73
G C 0.66
E C 0.92
END