PFRMAT SS
TARGET T0160
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0160.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0160.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0160.t2k.str.rdb  (weight 1.53983)
METHOD T0160.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 T0160.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0160
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 T0160.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 81
METHOD
METHOD ============================================
METHOD Comments from T0160.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0160
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 T0160.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 81
METHOD
METHOD ============================================
METHOD Comments from T0160.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0160
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 T0160.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 81
METHOD
METHOD ============================================
METHOD Comments from T0160.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0160
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 T0160.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 81
METHOD
METHOD ============================================
MODEL 1
G C 0.91
S C 0.85
H C 0.80
M C 0.75
A C 0.79
K C 0.82
H C 0.84
E C 0.80
Q C 0.76
I E 0.49
L E 0.80
V E 0.84
L E 0.82
D C 0.58
P C 0.83
P C 0.81
S C 0.75
D C 0.52
L E 0.82
K E 0.86
F E 0.80
K E 0.64
G C 0.55
P C 0.76
F C 0.82
T C 0.86
D C 0.81
V C 0.56
V E 0.74
T E 0.83
T E 0.88
N E 0.90
L E 0.92
K E 0.92
L E 0.91
Q E 0.85
N E 0.64
P C 0.80
S C 0.87
D C 0.84
R C 0.76
K E 0.59
V E 0.79
C E 0.89
F E 0.90
K E 0.92
V E 0.90
K E 0.85
T E 0.72
T C 0.66
A C 0.80
P C 0.78
R C 0.71
R E 0.59
Y E 0.75
C E 0.84
V E 0.80
R E 0.54
P C 0.74
N C 0.79
S C 0.64
G C 0.55
V E 0.73
I E 0.75
D C 0.73
P C 0.88
G C 0.93
S C 0.76
I E 0.58
V E 0.88
Y E 0.91
V E 0.92
S E 0.93
V E 0.92
M E 0.89
L E 0.76
Q C 0.56
P C 0.75
F C 0.79
D C 0.77
Y C 0.76
D C 0.83
P C 0.79
N C 0.72
E C 0.69
K C 0.66
S C 0.64
K C 0.73
H C 0.67
K E 0.78
F E 0.90
M E 0.92
V E 0.93
Q E 0.91
T E 0.90
I E 0.81
F E 0.68
A C 0.68
P C 0.84
P C 0.85
N C 0.84
I C 0.62
S C 0.53
D H 0.50
M H 0.80
E H 0.89
A H 0.93
V H 0.93
W H 0.92
K H 0.88
E H 0.77
A H 0.57
K C 0.72
P C 0.83
D C 0.84
E C 0.75
L C 0.54
M E 0.68
D E 0.82
S E 0.83
K E 0.85
P E 0.83
R E 0.86
C E 0.88
V E 0.88
F E 0.86
E E 0.72
M C 0.90
END