PFRMAT SS
TARGET T0627
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0627.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0627.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0627.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 T0627.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 45
METHOD
METHOD ============================================
METHOD Comments from T0627.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 45
METHOD
METHOD ============================================
METHOD Comments from T0627.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0627
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 T0627.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 45
METHOD
METHOD ============================================
MODEL 1
M C 0.96
I C 0.80
D C 0.68
T C 0.57
F C 0.46
E C 0.42
R C 0.52
T C 0.68
G C 0.82
P C 0.75
L C 0.54
M C 0.49
E C 0.51
A C 0.64
S C 0.81
S C 0.86
Y C 0.89
P H 0.77
A H 0.92
W H 0.94
A H 0.97
Q H 0.97
Q H 0.96
L H 0.96
I H 0.94
N H 0.88
D H 0.77
C H 0.65
S H 0.53
P H 0.89
A H 0.91
K H 0.93
A H 0.92
R H 0.88
V H 0.86
V H 0.73
E H 0.57
H C 0.58
E H 0.88
L H 0.94
Y H 0.96
Q H 0.95
Q H 0.93
M H 0.92
R H 0.78
D C 0.71
A C 0.91
K C 0.90
L C 0.78
S C 0.95
P H 0.93
Q H 0.96
I H 0.97
M H 0.97
R H 0.97
Q H 0.97
Y H 0.96
L H 0.94
I H 0.90
G H 0.75
G H 0.74
W H 0.83
P H 0.90
V H 0.95
V H 0.95
E H 0.94
Q H 0.90
F H 0.90
A H 0.95
V H 0.96
Y H 0.96
M H 0.96
A H 0.95
K H 0.94
N H 0.90
L H 0.85
T H 0.68
K H 0.52
T C 0.69
R C 0.70
F C 0.66
G C 0.57
R C 0.61
H C 0.68
P C 0.55
G C 0.61
E H 0.74
D H 0.91
M H 0.94
A H 0.95
R H 0.96
R H 0.96
W H 0.94
L H 0.93
M H 0.92
R H 0.86
N H 0.79
I H 0.75
R H 0.69
V H 0.65
E H 0.65
L H 0.79
N H 0.72
H H 0.82
A H 0.90
D H 0.94
Y H 0.96
W H 0.97
V H 0.97
N H 0.97
W H 0.98
C H 0.97
A H 0.97
A H 0.92
H H 0.51
D C 0.97
V C 0.97
T C 0.94
L H 0.94
E H 0.95
D H 0.95
L H 0.95
H H 0.87
D H 0.57
Q C 0.79
R C 0.89
V C 0.89
A C 0.87
P H 0.91
E H 0.94
L H 0.96
H H 0.96
A H 0.95
L H 0.96
S H 0.96
H H 0.95
W H 0.95
C H 0.95
W H 0.93
Q H 0.87
T H 0.74
S C 0.53
S C 0.70
S C 0.68
D C 0.72
S C 0.55
L H 0.94
A H 0.96
V H 0.96
A H 0.96
M H 0.97
A H 0.96
A H 0.95
T H 0.93
N H 0.92
Y H 0.92
A H 0.91
I H 0.89
E H 0.79
G H 0.59
A H 0.61
T H 0.60
G H 0.80
E H 0.89
W H 0.91
S H 0.88
A H 0.88
V H 0.85
V H 0.77
C H 0.66
S H 0.53
T C 0.49
G H 0.47
V H 0.46
Y H 0.52
A H 0.47
E C 0.51
A C 0.73
F C 0.84
A C 0.82
E C 0.56
E C 0.57
T C 0.62
R C 0.69
K H 0.73
K H 0.93
S H 0.96
M H 0.97
K H 0.97
W H 0.97
L H 0.97
K H 0.96
M H 0.95
H H 0.90
A H 0.82
Q H 0.67
Y H 0.64
D C 0.52
D C 0.55
A C 0.54
H C 0.72
P H 0.77
W H 0.90
E H 0.93
A H 0.96
L H 0.97
E H 0.97
I H 0.97
I H 0.97
C H 0.97
T H 0.95
L H 0.91
V H 0.76
G C 0.62
N C 0.80
K C 0.91
P C 0.88
S C 0.83
L H 0.84
Q H 0.90
L H 0.94
Q H 0.97
A H 0.97
E H 0.97
L H 0.97
R H 0.98
Q H 0.97
A H 0.97
V H 0.97
T H 0.97
K H 0.95
S H 0.96
Y H 0.97
D H 0.97
Y H 0.97
M H 0.97
Y H 0.97
L H 0.96
F H 0.95
L H 0.94
E H 0.90
R H 0.80
C H 0.69
I H 0.49
Q C 0.71
L C 0.49
D C 0.52
K C 0.52
V C 0.67
K C 0.74
S C 0.75
P C 0.73
R C 0.67
G C 0.49
R E 0.56
V E 0.67
A E 0.70
A E 0.69
L E 0.61
E C 0.59
M C 0.98
END