PFRMAT SS
TARGET T0177
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0177.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0177.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0177.t2k.str.rdb  (weight 1.53983)
METHOD T0177.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 T0177.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0177
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 T0177.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 63
METHOD
METHOD ============================================
METHOD Comments from T0177.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0177
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 T0177.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 63
METHOD
METHOD ============================================
METHOD Comments from T0177.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0177
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 T0177.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 63
METHOD
METHOD ============================================
METHOD Comments from T0177.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0177
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 T0177.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 63
METHOD
METHOD ============================================
MODEL 1
M C 0.91
G C 0.79
R C 0.68
A H 0.54
F H 0.73
E H 0.77
Y H 0.78
R H 0.87
R H 0.88
A H 0.86
A H 0.86
K H 0.81
E H 0.83
K H 0.88
R H 0.87
W H 0.87
D H 0.89
K H 0.87
M H 0.83
S H 0.82
K H 0.89
V H 0.92
F H 0.94
P H 0.95
K H 0.95
L H 0.96
A H 0.96
K H 0.96
A H 0.96
I H 0.96
T H 0.96
L H 0.96
A H 0.96
A H 0.95
K H 0.94
D H 0.63
G C 0.87
G C 0.91
S C 0.84
E C 0.83
P C 0.61
D C 0.65
T C 0.68
N C 0.74
A H 0.84
K H 0.89
L H 0.95
R H 0.96
T H 0.96
A H 0.96
I H 0.96
L H 0.96
N H 0.95
A H 0.94
K H 0.89
A H 0.83
Q C 0.56
N C 0.88
M C 0.92
P C 0.89
K H 0.66
D H 0.78
N H 0.85
I H 0.94
D H 0.95
A H 0.95
A H 0.95
I H 0.95
K H 0.91
R H 0.78
A H 0.52
S C 0.66
S C 0.84
K C 0.87
E C 0.85
G C 0.73
N C 0.57
L E 0.68
S E 0.78
E E 0.89
I E 0.89
T E 0.91
Y E 0.91
E E 0.89
G E 0.86
K E 0.80
A C 0.50
N C 0.84
F C 0.90
G C 0.78
V E 0.51
L E 0.82
I E 0.89
I E 0.91
M E 0.87
E E 0.79
C E 0.70
M E 0.50
T C 0.63
D C 0.83
N C 0.78
P C 0.54
T H 0.68
R H 0.78
T H 0.83
I H 0.94
A H 0.95
N H 0.94
L H 0.94
K H 0.95
S H 0.95
Y H 0.94
F H 0.92
N H 0.83
K H 0.70
T C 0.58
Q C 0.84
G C 0.78
A C 0.60
S C 0.56
I C 0.59
V C 0.72
P C 0.79
N C 0.84
G C 0.84
S C 0.59
L E 0.58
E E 0.57
F E 0.60
M E 0.61
F E 0.59
N E 0.45
R E 0.48
K E 0.48
S E 0.53
V E 0.83
F E 0.90
E E 0.89
C E 0.80
L E 0.59
K C 0.76
N C 0.90
E C 0.62
V C 0.59
E C 0.52
N C 0.66
L C 0.63
K C 0.68
L C 0.78
S C 0.84
L H 0.92
E H 0.94
D H 0.95
L H 0.95
E H 0.95
F H 0.95
A H 0.95
L H 0.95
I H 0.93
D H 0.86
Y C 0.50
G C 0.90
L C 0.79
E C 0.47
E E 0.35
L E 0.51
E E 0.59
E E 0.49
V C 0.57
E C 0.80
D C 0.80
K E 0.57
I E 0.85
I E 0.91
I E 0.91
R E 0.88
G E 0.62
D C 0.78
Y C 0.56
N H 0.57
S H 0.65
F H 0.88
K H 0.93
L H 0.94
L H 0.95
N H 0.96
E H 0.96
G H 0.96
F H 0.95
E H 0.95
S H 0.90
L C 0.61
K C 0.95
L C 0.89
P C 0.50
I E 0.67
L E 0.74
K E 0.76
A E 0.77
S E 0.85
L E 0.87
Q E 0.83
R E 0.82
I E 0.58
A C 0.65
T C 0.80
T C 0.71
P C 0.59
I E 0.58
E E 0.62
L C 0.69
N C 0.88
D H 0.83
E H 0.88
Q H 0.91
M H 0.95
E H 0.95
L H 0.94
T H 0.95
E H 0.96
K H 0.95
L H 0.95
L H 0.95
D H 0.93
R H 0.87
I H 0.79
E H 0.57
D C 0.58
D C 0.65
D C 0.55
D C 0.52
V H 0.45
V H 0.43
A E 0.41
L E 0.41
Y E 0.38
T C 0.51
N C 0.70
I C 0.77
E C 0.91
END