PFRMAT SS
TARGET T0169
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0169.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0169.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0169.t2k.str.rdb  (weight 1.53983)
METHOD T0169.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 T0169.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0169
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 T0169.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 246
METHOD
METHOD ============================================
METHOD Comments from T0169.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0169
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 T0169.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 246
METHOD
METHOD ============================================
METHOD Comments from T0169.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0169
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 T0169.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 246
METHOD
METHOD ============================================
METHOD Comments from T0169.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0169
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 T0169.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 246
METHOD
METHOD ============================================
MODEL 1
M C 0.87
D E 0.50
I E 0.62
R E 0.54
T C 0.55
I C 0.80
T C 0.89
S H 0.64
S H 0.64
D H 0.68
Y H 0.90
E H 0.92
M H 0.93
V H 0.95
T H 0.95
S H 0.94
V H 0.93
L H 0.91
N H 0.83
E H 0.71
W C 0.48
W C 0.75
G C 0.74
G C 0.69
R C 0.61
Q C 0.49
L H 0.52
K H 0.67
E H 0.83
K H 0.87
L H 0.89
P H 0.91
R H 0.92
L H 0.91
F H 0.90
F H 0.84
E H 0.66
H C 0.64
F C 0.80
Q C 0.82
D C 0.81
T C 0.52
S E 0.85
F E 0.92
I E 0.92
T E 0.91
S E 0.84
E E 0.59
H C 0.92
N C 0.92
S E 0.77
M E 0.91
T E 0.88
G E 0.92
F E 0.93
L E 0.93
I E 0.92
G E 0.88
F E 0.80
Q E 0.58
S C 0.70
Q C 0.77
S C 0.78
D C 0.74
P C 0.72
E C 0.60
T E 0.70
A E 0.84
Y E 0.88
I E 0.90
H E 0.84
F E 0.88
S E 0.87
G E 0.89
V E 0.77
H C 0.68
P H 0.61
D H 0.62
F H 0.72
R C 0.55
K C 0.71
M C 0.70
Q C 0.68
I H 0.65
G H 0.87
K H 0.95
Q H 0.96
L H 0.96
Y H 0.96
D H 0.96
V H 0.96
F H 0.96
I H 0.96
E H 0.96
T H 0.95
V H 0.95
K H 0.94
Q H 0.83
R C 0.72
G C 0.95
C C 0.88
T C 0.57
R E 0.89
V E 0.92
K E 0.92
C E 0.89
V E 0.81
T E 0.61
S C 0.72
P C 0.81
V C 0.82
N C 0.71
K H 0.83
V H 0.92
S H 0.95
I H 0.96
A H 0.96
Y H 0.96
H H 0.95
T H 0.93
K H 0.83
L C 0.57
G C 0.92
F C 0.77
D E 0.65
I E 0.77
E E 0.75
K E 0.73
G E 0.76
T E 0.77
K E 0.68
T C 0.51
V C 0.68
N C 0.78
G C 0.69
I C 0.49
S E 0.64
V E 0.71
F E 0.69
A E 0.64
N E 0.53
Y C 0.57
D C 0.80
G C 0.87
P C 0.83
G C 0.66
Q C 0.53
D C 0.41
R H 0.45
V E 0.47
L E 0.50
F E 0.48
V E 0.44
K C 0.43
N C 0.72
I C 0.92
END