PFRMAT SS
TARGET T0578
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0578.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0578.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0578.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 T0578.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 28
METHOD
METHOD ============================================
METHOD Comments from T0578.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 28
METHOD
METHOD ============================================
METHOD Comments from T0578.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0578
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 T0578.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 28
METHOD
METHOD ============================================
MODEL 1
S C 0.86
N H 0.51
A H 0.68
M H 0.68
K H 0.71
K H 0.62
A H 0.62
T C 0.65
M H 0.75
L H 0.92
T H 0.94
Y H 0.96
L H 0.96
E H 0.96
E H 0.96
Q H 0.95
L H 0.92
E H 0.83
K H 0.63
H C 0.66
L C 0.82
G C 0.85
D C 0.82
Y C 0.68
E C 0.48
V E 0.70
G E 0.78
L E 0.71
D E 0.59
W C 0.64
D C 0.70
R C 0.72
K C 0.81
N C 0.84
H C 0.65
T E 0.77
I E 0.94
E E 0.96
V E 0.96
I E 0.97
V E 0.98
R E 0.98
L E 0.97
Y E 0.97
A E 0.92
E E 0.78
N C 0.50
N C 0.76
E C 0.83
Q C 0.62
V E 0.61
A E 0.89
I E 0.93
D E 0.92
D E 0.52
V C 0.76
D C 0.86
G C 0.81
T C 0.54
L E 0.64
S C 0.72
E C 0.84
E C 0.83
E C 0.69
F E 0.58
I E 0.77
E E 0.81
F E 0.65
E E 0.54
D E 0.49
G E 0.77
L E 0.91
L E 0.93
F E 0.84
Y E 0.64
N C 0.82
P C 0.82
Q C 0.79
K C 0.63
S C 0.77
V C 0.71
V C 0.70
D C 0.84
D H 0.53
E C 0.56
E C 0.57
Y C 0.53
L E 0.76
V E 0.90
T E 0.89
I E 0.77
P E 0.51
Y C 0.79
E C 0.87
G C 0.88
K C 0.82
K C 0.80
G C 0.80
L C 0.67
R C 0.49
K H 0.95
A H 0.96
V H 0.97
L H 0.98
D H 0.98
G H 0.97
F H 0.98
I H 0.98
H H 0.98
Y H 0.97
L H 0.97
K H 0.97
V H 0.97
V H 0.97
L H 0.95
D H 0.85
E H 0.57
G C 0.74
Q H 0.64
S H 0.78
D H 0.80
L H 0.87
L H 0.88
D H 0.88
F H 0.78
L H 0.49
S C 0.80
D C 0.92
E C 0.87
T C 0.82
A C 0.77
E C 0.67
V E 0.69
F E 0.89
E E 0.92
L E 0.90
H E 0.83
W C 0.50
E C 0.89
P H 0.86
A H 0.93
D H 0.94
F H 0.95
E H 0.95
A H 0.94
M H 0.92
I H 0.90
K H 0.83
K H 0.73
V H 0.66
A H 0.70
E H 0.71
T H 0.59
E H 0.50
K C 0.67
E C 0.72
Q C 0.75
W C 0.84
I C 0.90
A C 0.90
Y C 0.90
P C 0.90
S C 0.91
Y C 0.99
END