PFRMAT SS
TARGET T0193
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0193.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0193.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0193.t2k.str.rdb  (weight 1.53983)
METHOD T0193.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 T0193.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0193
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 T0193.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 18
METHOD
METHOD ============================================
METHOD Comments from T0193.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0193
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 T0193.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 18
METHOD
METHOD ============================================
METHOD Comments from T0193.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0193
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 T0193.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 18
METHOD
METHOD ============================================
METHOD Comments from T0193.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0193
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 T0193.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 18
METHOD
METHOD ============================================
MODEL 1
M C 0.86
K C 0.80
V C 0.79
P C 0.75
E H 0.87
A H 0.90
A H 0.90
I H 0.91
S H 0.86
R H 0.81
L H 0.77
I H 0.91
T H 0.94
Y H 0.95
L H 0.95
R H 0.96
I H 0.95
L H 0.95
E H 0.95
E H 0.94
L H 0.93
E H 0.90
A H 0.80
Q C 0.62
G C 0.93
V C 0.87
H C 0.61
R E 0.60
T E 0.57
S C 0.68
S H 0.74
E H 0.92
Q H 0.93
L H 0.94
G H 0.94
E H 0.92
L H 0.87
A H 0.57
Q C 0.89
V C 0.90
T C 0.92
A H 0.88
F H 0.93
Q H 0.92
V H 0.93
R H 0.89
K H 0.88
D H 0.79
L H 0.80
S H 0.78
Y H 0.68
F H 0.50
G C 0.57
S C 0.57
Y C 0.71
G C 0.82
T C 0.79
R C 0.66
G C 0.68
V C 0.63
G C 0.60
Y C 0.55
T C 0.64
V H 0.90
P H 0.95
V H 0.95
L H 0.95
K H 0.95
R H 0.95
E H 0.95
L H 0.95
R H 0.95
H H 0.93
I H 0.87
L H 0.52
G C 0.88
L C 0.83
N C 0.81
R C 0.70
K C 0.59
W E 0.52
G E 0.69
L E 0.90
C E 0.93
I E 0.93
V E 0.86
G E 0.71
M C 0.72
G C 0.80
R H 0.62
L H 0.89
G H 0.93
S H 0.93
A H 0.93
L H 0.89
A H 0.79
D H 0.58
Y C 0.59
P C 0.58
G C 0.61
F C 0.67
G C 0.78
E C 0.83
S C 0.82
F E 0.58
E E 0.86
L E 0.92
R E 0.88
G E 0.90
F E 0.88
F E 0.84
D E 0.69
V C 0.62
D C 0.79
P C 0.62
E C 0.65
K C 0.52
V C 0.66
G C 0.62
R E 0.64
P E 0.69
V C 0.51
R C 0.86
G C 0.89
G C 0.50
V E 0.75
I E 0.74
E E 0.59
H C 0.64
V H 0.66
D H 0.80
L H 0.81
L H 0.82
P H 0.81
Q H 0.80
R H 0.74
V H 0.55
P C 0.57
G C 0.77
R C 0.89
I C 0.81
E E 0.54
I E 0.92
A E 0.93
L E 0.93
L E 0.88
T E 0.70
V C 0.69
P C 0.87
R H 0.70
E H 0.87
A H 0.91
A H 0.93
Q H 0.94
K H 0.94
A H 0.95
A H 0.96
D H 0.96
L H 0.96
L H 0.96
V H 0.95
A H 0.92
A C 0.53
G C 0.93
I C 0.89
K C 0.70
G E 0.78
I E 0.89
L E 0.86
N E 0.67
F C 0.68
A C 0.75
P C 0.63
V E 0.58
V E 0.73
L E 0.58
E E 0.54
V C 0.63
P C 0.81
K C 0.84
E C 0.84
V C 0.50
A E 0.85
V E 0.89
E E 0.81
N E 0.79
V E 0.62
D C 0.61
F H 0.49
L H 0.61
A H 0.76
G H 0.84
L H 0.91
T H 0.95
R H 0.95
L H 0.96
S H 0.96
F H 0.95
A H 0.93
I H 0.83
L H 0.56
N C 0.74
P H 0.73
K H 0.80
W H 0.84
R H 0.84
E H 0.80
E H 0.76
M H 0.57
M C 0.63
G C 0.92
END