PFRMAT SS
TARGET T0561
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0561.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0561.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0561.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 T0561.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0561
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 T0561.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 4
METHOD
METHOD ============================================
METHOD Comments from T0561.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0561
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 T0561.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 4
METHOD
METHOD ============================================
METHOD Comments from T0561.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0561
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 T0561.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 4
METHOD
METHOD ============================================
MODEL 1
V C 0.94
E C 0.80
K C 0.63
K C 0.52
K H 0.49
Y H 0.49
L H 0.48
D H 0.50
S H 0.77
E H 0.80
F H 0.79
L H 0.83
L H 0.82
H H 0.79
C H 0.70
I H 0.58
S H 0.50
A H 0.92
Q H 0.94
L H 0.96
L H 0.97
D H 0.96
M H 0.96
W H 0.97
K H 0.96
Q H 0.95
A H 0.94
R H 0.94
A H 0.96
R H 0.95
W H 0.96
L H 0.96
E H 0.96
L H 0.94
V H 0.91
G H 0.91
K H 0.93
E H 0.93
W H 0.94
A H 0.95
H H 0.93
M H 0.91
L H 0.86
A H 0.71
L H 0.49
N C 0.93
P C 0.77
E C 0.73
R C 0.66
K C 0.73
D C 0.66
F E 0.47
L E 0.54
W E 0.50
K C 0.59
N C 0.74
Q C 0.79
S C 0.72
E C 0.58
M H 0.48
N H 0.59
S H 0.66
A H 0.73
F H 0.79
F H 0.79
D H 0.76
L H 0.84
C H 0.89
E H 0.92
V H 0.95
G H 0.95
K H 0.95
Q H 0.94
V H 0.94
M H 0.89
L H 0.84
G H 0.72
L H 0.56
L C 0.58
G C 0.84
K C 0.81
E C 0.74
V C 0.78
A C 0.86
L C 0.92
P C 0.51
K H 0.74
E H 0.76
E H 0.79
Q H 0.82
A H 0.87
F H 0.93
W H 0.97
I H 0.97
M H 0.97
Y H 0.97
A H 0.97
V H 0.95
H H 0.90
L H 0.86
S H 0.81
A H 0.85
A H 0.83
C H 0.81
A H 0.84
E H 0.80
E H 0.72
L C 0.50
H C 0.79
M C 0.88
E C 0.76
V C 0.71
A C 0.68
M C 0.70
S C 0.68
L C 0.46
R C 0.36
K E 0.47
L E 0.45
N E 0.54
V E 0.61
K E 0.65
L E 0.56
K C 0.58
D C 0.74
F C 0.73
N C 0.73
F C 0.78
G C 0.80
G C 0.67
T C 0.58
R E 0.39
Y E 0.38
F C 0.50
K C 0.72
D C 0.85
M C 0.92
P C 0.92
P H 0.63
E H 0.80
E H 0.81
K H 0.84
K H 0.86
R H 0.86
R H 0.87
M H 0.88
E H 0.89
R H 0.89
K H 0.91
Q H 0.92
R H 0.92
I H 0.95
E H 0.95
E H 0.95
A H 0.93
R H 0.91
R H 0.83
H H 0.59
G C 0.77
M C 0.94
P C 0.99
END