PFRMAT SS
TARGET T0171
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0171.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0171.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0171.t2k.str.rdb  (weight 1.53983)
METHOD T0171.t2k.alpha.rdb  (weight 0.659012)
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 T0171.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0171
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 T0171.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 704
METHOD
METHOD ============================================
METHOD Comments from T0171.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0171
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 T0171.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 704
METHOD
METHOD ============================================
METHOD Comments from T0171.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0171
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 T0171.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 704
METHOD
METHOD ============================================
METHOD Comments from T0171.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0171
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    5	   15
METHOD	    7	   15
METHOD	    9	   15
METHOD	   13	   11 (1 ABCDEFGHIST )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0171.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 704
METHOD
METHOD ============================================
MODEL 1
M C 0.90
N C 0.55
N E 0.81
I E 0.88
W E 0.90
W E 0.90
Q E 0.85
T E 0.76
K C 0.64
G C 0.85
Q C 0.86
G C 0.88
N C 0.87
V C 0.83
H E 0.65
L E 0.93
V E 0.93
L E 0.93
L E 0.88
H E 0.49
G C 0.81
W C 0.83
G C 0.79
L C 0.74
N C 0.75
A H 0.56
E H 0.65
V H 0.69
W H 0.83
R H 0.90
C H 0.90
I H 0.90
D H 0.91
E H 0.91
E H 0.86
L H 0.81
S H 0.67
S C 0.68
H C 0.89
F C 0.75
T E 0.62
L E 0.92
H E 0.92
L E 0.90
V E 0.79
D C 0.57
L C 0.82
P C 0.80
G C 0.79
F C 0.79
G C 0.79
R C 0.79
S C 0.79
R C 0.82
G C 0.84
F C 0.83
G C 0.82
A C 0.79
L C 0.80
S C 0.82
L H 0.92
A H 0.94
D H 0.95
M H 0.95
A H 0.94
E H 0.93
A H 0.91
V H 0.91
L H 0.87
Q H 0.71
Q C 0.64
A C 0.88
P C 0.89
D C 0.84
K E 0.53
A E 0.89
I E 0.93
W E 0.93
L E 0.89
G E 0.71
W C 0.63
S C 0.73
L H 0.75
G H 0.92
G H 0.95
L H 0.96
V H 0.96
A H 0.96
S H 0.96
Q H 0.96
I H 0.95
A H 0.94
L H 0.88
T H 0.71
H C 0.76
P H 0.54
E C 0.54
R H 0.55
V C 0.46
Q E 0.62
A E 0.84
L E 0.91
V E 0.92
T E 0.89
V E 0.77
A C 0.51
S C 0.72
S C 0.75
P C 0.76
C C 0.74
F C 0.71
S C 0.70
A C 0.68
R C 0.64
D C 0.58
E C 0.54
W C 0.50
P H 0.50
G H 0.54
I H 0.53
K H 0.62
P H 0.77
D H 0.78
V H 0.80
L H 0.79
A H 0.77
G H 0.74
F H 0.70
Q H 0.69
Q H 0.63
Q H 0.53
L C 0.50
S C 0.51
D H 0.51
D H 0.50
F H 0.73
Q H 0.82
R H 0.82
T H 0.83
V H 0.83
E H 0.82
R H 0.77
F H 0.73
L H 0.69
A H 0.62
L H 0.52
Q C 0.48
T C 0.54
M C 0.62
G C 0.61
T C 0.61
E C 0.68
T C 0.76
A C 0.75
R H 0.88
Q H 0.91
D H 0.92
A H 0.94
R H 0.93
A H 0.93
L H 0.91
K H 0.90
K H 0.85
T H 0.78
V H 0.64
L H 0.51
A C 0.58
L C 0.61
P C 0.62
M C 0.52
P H 0.49
E H 0.57
V H 0.81
D H 0.87
V H 0.88
L H 0.89
N H 0.88
G H 0.87
G H 0.85
L H 0.83
E H 0.79
I H 0.74
L H 0.63
K H 0.54
T C 0.52
V C 0.51
D C 0.51
L H 0.59
R H 0.71
Q H 0.71
P H 0.69
L H 0.65
Q H 0.52
N C 0.64
V C 0.79
S C 0.84
M C 0.82
P C 0.72
F E 0.88
L E 0.93
R E 0.93
L E 0.91
Y E 0.72
G C 0.72
Y C 0.81
L C 0.82
D C 0.82
G C 0.78
L C 0.73
V C 0.79
P C 0.84
R H 0.81
K H 0.88
V H 0.91
V H 0.93
P H 0.94
M H 0.94
L H 0.94
D H 0.93
K H 0.84
L H 0.66
W C 0.84
P C 0.86
H C 0.90
S C 0.71
E E 0.71
S E 0.90
Y E 0.91
I E 0.88
F E 0.60
A C 0.81
K C 0.90
A C 0.82
A C 0.80
H C 0.74
A C 0.72
P C 0.61
F C 0.49
I H 0.50
S C 0.55
H C 0.73
P H 0.87
A H 0.93
E H 0.95
F H 0.95
C H 0.96
H H 0.96
L H 0.96
L H 0.95
V H 0.95
A H 0.94
L H 0.93
K H 0.88
Q H 0.72
R C 0.51
V C 0.90
END