PFRMAT SS
TARGET T0454
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0454.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0454.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0454.t2k.str.rdb  (weight 1.53983)
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 T0454.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 1474
METHOD
METHOD ============================================
METHOD Comments from T0454.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 1474
METHOD
METHOD ============================================
METHOD Comments from T0454.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0454
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 T0454.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 1474
METHOD
METHOD ============================================
MODEL 1
M C 0.97
T C 0.91
R H 0.57
A H 0.77
D H 0.82
C H 0.84
R H 0.95
S H 0.97
R H 0.97
L H 0.97
M H 0.98
E H 0.98
V H 0.98
A H 0.98
T H 0.98
E H 0.97
L H 0.97
F H 0.97
A H 0.96
Q H 0.88
K H 0.55
G C 0.90
F C 0.89
Y C 0.79
G C 0.67
V C 0.60
S C 0.63
I H 0.95
R H 0.97
E H 0.97
L H 0.98
A H 0.97
Q H 0.96
A H 0.90
A C 0.51
G C 0.98
A C 0.97
S C 0.94
I H 0.74
S H 0.82
M H 0.80
I H 0.82
S H 0.81
Y H 0.76
H H 0.59
F C 0.67
G C 0.86
G C 0.90
K H 0.91
E H 0.94
G H 0.97
L H 0.97
Y H 0.98
A H 0.98
A H 0.97
V H 0.97
L H 0.97
Q H 0.95
E H 0.92
Q H 0.90
F H 0.87
A H 0.88
C H 0.88
F H 0.89
G H 0.90
Q H 0.89
L H 0.89
D H 0.87
D H 0.83
I H 0.75
R H 0.64
G C 0.55
Q C 0.69
A C 0.85
G C 0.92
D C 0.93
P H 0.90
L H 0.95
A H 0.97
V H 0.97
M H 0.97
T H 0.97
A H 0.97
Y H 0.97
L H 0.97
R H 0.97
W H 0.97
T H 0.97
I H 0.96
Q H 0.94
R H 0.89
H H 0.83
R H 0.66
N C 0.50
N C 0.82
P H 0.57
Q H 0.71
L H 0.88
L H 0.92
R H 0.92
F H 0.92
Y H 0.93
T H 0.92
S H 0.92
E H 0.88
L H 0.78
T H 0.60
N C 0.62
P C 0.74
T C 0.68
P H 0.69
C H 0.77
F H 0.84
A H 0.89
A H 0.91
I H 0.93
V H 0.93
S H 0.91
P H 0.90
A H 0.87
I H 0.88
A H 0.89
S H 0.90
V H 0.93
I H 0.95
R H 0.96
L H 0.96
L H 0.97
A H 0.97
E H 0.97
S H 0.97
I H 0.97
E H 0.97
A H 0.96
G H 0.94
M H 0.93
T H 0.86
R H 0.53
G C 0.88
L C 0.89
F C 0.83
R C 0.86
R C 0.83
D C 0.87
L C 0.92
H C 0.94
A H 0.95
V H 0.97
N H 0.97
S H 0.98
A H 0.98
L H 0.98
A H 0.98
L H 0.97
A H 0.97
G H 0.97
M H 0.97
V H 0.96
N H 0.95
Y H 0.94
F H 0.94
F H 0.92
L H 0.87
S H 0.80
T H 0.80
L H 0.81
A H 0.80
T H 0.79
E H 0.75
G H 0.72
L H 0.62
T C 0.57
S C 0.80
H C 0.78
S C 0.76
P C 0.69
D C 0.76
Q C 0.74
D H 0.91
E H 0.94
E H 0.95
L H 0.97
I H 0.97
R H 0.97
Q H 0.97
Y H 0.97
V H 0.96
A H 0.96
I H 0.97
F H 0.98
T H 0.98
R H 0.97
G H 0.97
I H 0.96
M H 0.88
A H 0.75
D C 0.52
G C 0.81
G C 0.88
A C 0.89
A C 0.88
P C 0.93
A C 0.98
END