PFRMAT SS
TARGET T0489
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0489.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0489.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0489.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 T0489.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0489
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 T0489.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 154
METHOD
METHOD ============================================
METHOD Comments from T0489.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0489
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 T0489.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 154
METHOD
METHOD ============================================
METHOD Comments from T0489.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0489
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 T0489.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 154
METHOD
METHOD ============================================
MODEL 1
M C 0.97
M C 0.65
F C 0.56
K C 0.48
W H 0.52
P H 0.56
W H 0.57
K H 0.58
A H 0.54
D C 0.54
D C 0.69
E C 0.83
S C 0.91
G C 0.96
N C 0.96
A H 0.84
E H 0.88
M H 0.93
P H 0.96
W H 0.95
E H 0.96
Q H 0.95
A H 0.94
L H 0.77
A H 0.59
I C 0.74
P C 0.68
V H 0.65
L H 0.82
A H 0.67
H C 0.57
L C 0.95
S C 0.97
S H 0.93
T H 0.96
E H 0.97
Q H 0.97
H H 0.97
K H 0.97
L H 0.97
T H 0.98
Q H 0.98
M H 0.97
A H 0.98
A H 0.97
R H 0.97
F H 0.95
L H 0.91
Q H 0.81
Q H 0.64
K C 0.54
R C 0.59
L E 0.48
V E 0.57
A C 0.53
L C 0.75
Q C 0.89
G C 0.89
L C 0.68
E E 0.53
L C 0.59
T C 0.93
P H 0.94
L H 0.96
H H 0.97
Q H 0.98
A H 0.98
R H 0.98
I H 0.98
A H 0.98
M H 0.97
L H 0.97
F H 0.96
C H 0.97
L H 0.97
P H 0.96
V H 0.94
L H 0.86
E H 0.57
L C 0.71
G C 0.69
I H 0.64
E H 0.62
W H 0.57
L C 0.59
D C 0.73
G C 0.83
F C 0.74
H E 0.52
E E 0.95
V E 0.97
L E 0.98
I E 0.94
Y E 0.61
P C 0.78
A C 0.84
P C 0.71
F C 0.61
I E 0.48
V E 0.48
D C 0.60
D C 0.53
E E 0.45
W E 0.47
E E 0.45
D C 0.65
D C 0.77
I C 0.83
G C 0.73
L E 0.60
V E 0.78
H E 0.53
N C 0.62
Q C 0.66
R C 0.52
V E 0.49
V E 0.57
Q E 0.63
S E 0.53
G C 0.46
Q C 0.44
S C 0.49
W C 0.52
Q C 0.65
Q C 0.76
G C 0.84
P C 0.62
V E 0.87
V E 0.91
L E 0.80
N C 0.61
W H 0.76
L H 0.91
D H 0.91
I H 0.92
Q H 0.86
D H 0.56
S C 0.75
F C 0.89
D C 0.87
A C 0.86
S C 0.85
G C 0.83
F C 0.70
N C 0.40
L H 0.53
V H 0.79
V H 0.90
H H 0.92
E H 0.92
V H 0.94
A H 0.95
H H 0.95
K H 0.94
L H 0.89
D H 0.76
T H 0.66
R C 0.57
N C 0.77
G C 0.83
D C 0.80
R C 0.79
A C 0.87
S C 0.90
G C 0.87
V C 0.83
P C 0.79
L C 0.79
I C 0.79
P C 0.73
L C 0.67
R C 0.66
E C 0.62
V H 0.83
A H 0.91
G H 0.94
W H 0.96
E H 0.96
H H 0.95
D H 0.94
L H 0.94
H H 0.95
A H 0.96
A H 0.96
M H 0.96
N H 0.96
N H 0.94
I H 0.95
Q H 0.95
D H 0.95
E H 0.95
I H 0.94
D H 0.92
L H 0.84
V H 0.65
G C 0.68
E C 0.76
S C 0.73
A C 0.70
A C 0.70
S C 0.64
I C 0.60
D C 0.69
A H 0.63
Y H 0.59
A H 0.52
A C 0.54
T C 0.70
D C 0.86
P H 0.85
A H 0.93
E H 0.94
C H 0.95
F H 0.95
A H 0.95
V H 0.94
L H 0.92
S H 0.92
E H 0.91
Y H 0.86
F H 0.79
F H 0.66
S C 0.46
A C 0.76
P H 0.71
E H 0.89
L H 0.92
F H 0.91
A H 0.90
P H 0.80
R H 0.77
F H 0.57
P H 0.92
A H 0.95
L H 0.97
W H 0.97
Q H 0.98
R H 0.97
F H 0.97
C H 0.97
H H 0.96
F H 0.93
Y H 0.81
R H 0.55
Q C 0.60
D C 0.92
P H 0.86
L H 0.92
A H 0.92
R H 0.91
R H 0.84
R H 0.76
E H 0.70
N H 0.59
G H 0.58
L H 0.50
Q C 0.63
D C 0.81
E C 0.70
G C 0.66
D C 0.51
R C 0.40
R E 0.43
I E 0.44
V C 0.53
H C 0.96
END