PFRMAT SS
TARGET T0144
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0144.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0144.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0144.t2k.str.rdb  (weight 1.53983)
METHOD T0144.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 T0144.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0144
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 T0144.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 396
METHOD
METHOD ============================================
METHOD Comments from T0144.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0144
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 T0144.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 396
METHOD
METHOD ============================================
METHOD Comments from T0144.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0144
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 T0144.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 396
METHOD
METHOD ============================================
METHOD Comments from T0144.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0144
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 T0144.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 396
METHOD
METHOD ============================================
MODEL 1
M C 0.92
S C 0.79
N C 0.86
P C 0.78
K E 0.55
V E 0.83
F E 0.85
F E 0.85
D E 0.78
M E 0.75
A E 0.74
I E 0.63
A C 0.70
G C 0.74
N C 0.56
P E 0.60
A E 0.62
G E 0.60
R E 0.82
I E 0.90
V E 0.92
M E 0.91
E E 0.90
L E 0.81
Y C 0.49
A C 0.49
D C 0.56
T C 0.57
T C 0.78
P H 0.67
R H 0.85
T H 0.92
A H 0.95
E H 0.95
N H 0.94
F H 0.95
R H 0.95
A H 0.94
L H 0.91
C H 0.79
T C 0.49
G C 0.80
E C 0.77
K C 0.71
G C 0.71
V C 0.66
G C 0.77
R C 0.80
S C 0.88
G C 0.87
K C 0.73
P E 0.49
L C 0.58
H C 0.64
Y C 0.68
K C 0.75
G C 0.79
S C 0.65
T E 0.54
F E 0.64
H E 0.67
R E 0.69
V E 0.65
I C 0.51
P C 0.74
N C 0.79
F E 0.47
M E 0.74
C E 0.75
Q E 0.59
G C 0.62
G C 0.75
D C 0.79
F C 0.79
T C 0.76
A C 0.80
G C 0.82
N C 0.81
G C 0.84
T C 0.82
G C 0.84
A C 0.78
E C 0.63
S C 0.55
I C 0.54
Y C 0.67
G C 0.77
A C 0.73
K C 0.62
F C 0.64
A C 0.69
D C 0.69
E C 0.61
N C 0.64
F C 0.65
I C 0.65
K C 0.66
R C 0.69
H C 0.72
T C 0.79
G C 0.86
P C 0.80
G C 0.60
I E 0.71
L E 0.79
S E 0.75
M E 0.72
A E 0.59
N C 0.52
A C 0.72
G C 0.86
A C 0.84
G C 0.83
T C 0.81
N C 0.82
G C 0.79
S C 0.61
Q E 0.72
F E 0.86
F E 0.88
I E 0.88
C E 0.83
T E 0.62
E C 0.60
K C 0.76
T C 0.78
E C 0.66
W C 0.63
L C 0.70
D C 0.84
G C 0.87
K C 0.77
H E 0.68
V E 0.80
V E 0.86
F E 0.79
G E 0.74
K E 0.73
V E 0.61
I C 0.49
E C 0.61
G C 0.62
M H 0.63
N H 0.77
V H 0.93
V H 0.95
R H 0.95
D H 0.95
I H 0.94
E H 0.91
K H 0.78
V C 0.50
G C 0.82
S C 0.86
G C 0.84
S C 0.89
G C 0.91
K C 0.82
T C 0.63
S C 0.67
R C 0.61
P C 0.53
V E 0.72
T E 0.86
I E 0.85
A E 0.64
D C 0.51
C C 0.68
G C 0.59
Q C 0.53
L C 0.73
S C 0.92
END