PFRMAT SS
TARGET T0175
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0175.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0175.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0175.t2k.str.rdb  (weight 1.53983)
METHOD T0175.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 T0175.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0175
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 T0175.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 561
METHOD
METHOD ============================================
METHOD Comments from T0175.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0175
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 T0175.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 561
METHOD
METHOD ============================================
METHOD Comments from T0175.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0175
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 T0175.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 561
METHOD
METHOD ============================================
METHOD Comments from T0175.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0175
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 T0175.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 561
METHOD
METHOD ============================================
MODEL 1
M C 0.88
D C 0.77
I C 0.67
P C 0.59
R C 0.55
I C 0.56
F C 0.54
T C 0.52
I C 0.54
S C 0.53
E C 0.56
S C 0.61
E C 0.60
H C 0.64
R C 0.63
I C 0.64
H C 0.60
N C 0.54
P H 0.68
F H 0.67
T H 0.76
E H 0.90
E H 0.91
K H 0.93
Y H 0.95
A H 0.95
T H 0.95
L H 0.95
G H 0.95
R H 0.92
V H 0.85
L H 0.50
R C 0.86
M C 0.90
K C 0.92
P C 0.86
G C 0.90
T C 0.70
R E 0.79
I E 0.88
L E 0.88
D E 0.85
L E 0.52
G C 0.68
S C 0.79
G C 0.77
S C 0.59
G H 0.60
E H 0.94
M H 0.95
L H 0.96
C H 0.96
T H 0.96
W H 0.96
A H 0.95
R H 0.91
D H 0.80
H C 0.58
G C 0.93
I C 0.83
T E 0.65
G E 0.89
T E 0.88
G E 0.90
I E 0.84
D E 0.52
M C 0.86
S C 0.91
S H 0.91
L H 0.94
F H 0.95
T H 0.96
A H 0.96
Q H 0.96
A H 0.95
K H 0.96
R H 0.95
R H 0.95
A H 0.95
E H 0.94
E H 0.89
L C 0.50
G C 0.91
V C 0.86
S C 0.77
E C 0.73
R C 0.73
V E 0.63
H E 0.87
F E 0.90
I E 0.87
H E 0.78
N C 0.53
D C 0.69
A H 0.52
A H 0.53
G H 0.48
Y C 0.78
V C 0.79
A C 0.76
N C 0.70
E C 0.76
K C 0.82
C C 0.82
D C 0.72
V E 0.91
A E 0.93
A E 0.92
C E 0.85
V C 0.56
G C 0.52
A H 0.53
T H 0.67
W H 0.62
I C 0.53
A C 0.81
G C 0.81
G C 0.82
F H 0.83
A H 0.92
G H 0.95
A H 0.95
E H 0.96
E H 0.96
L H 0.95
L H 0.95
A H 0.94
Q H 0.87
S H 0.63
L C 0.62
K C 0.83
P C 0.69
G C 0.73
G E 0.54
I E 0.86
M E 0.93
L E 0.92
I E 0.90
G E 0.78
E E 0.55
P C 0.65
Y C 0.74
W C 0.72
R C 0.71
Q C 0.69
L C 0.68
P C 0.65
A C 0.58
T C 0.54
E C 0.47
E H 0.49
I H 0.52
A H 0.55
Q H 0.56
A H 0.56
C H 0.53
G C 0.45
V C 0.55
S C 0.66
S C 0.70
T C 0.70
S C 0.70
D C 0.71
F C 0.79
L C 0.83
T C 0.87
L H 0.90
P H 0.94
G H 0.95
L H 0.96
V H 0.96
G H 0.96
A H 0.96
F H 0.95
D H 0.93
D H 0.83
L C 0.63
G C 0.94
Y C 0.84
D E 0.59
V E 0.80
V E 0.83
E E 0.81
M E 0.77
V E 0.67
L E 0.54
A C 0.58
D C 0.66
Q C 0.60
E C 0.63
G C 0.63
W H 0.48
D H 0.56
R H 0.55
Y H 0.54
E H 0.58
A H 0.70
A H 0.75
K H 0.80
W H 0.85
L H 0.85
T H 0.87
M H 0.92
R H 0.94
R H 0.94
W H 0.93
L H 0.92
E H 0.85
A H 0.70
N H 0.56
P H 0.63
D H 0.67
D H 0.68
D H 0.80
F H 0.84
A H 0.89
A H 0.91
E H 0.90
V H 0.90
R H 0.89
A H 0.87
E H 0.85
L H 0.78
N H 0.70
I H 0.61
A C 0.49
P H 0.62
K H 0.80
R H 0.85
Y H 0.88
V H 0.92
T H 0.93
Y H 0.94
A H 0.95
R H 0.95
E H 0.95
C H 0.95
F H 0.94
G H 0.94
W H 0.94
G H 0.94
V H 0.93
F H 0.90
A H 0.85
L H 0.77
I H 0.58
A C 0.61
R C 0.91
END