PFRMAT SS
TARGET T0190
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0190.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0190.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0190.t2k.str.rdb  (weight 1.53983)
METHOD T0190.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 T0190.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0190
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 T0190.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 36
METHOD
METHOD ============================================
METHOD Comments from T0190.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0190
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 T0190.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 36
METHOD
METHOD ============================================
METHOD Comments from T0190.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0190
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 T0190.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 36
METHOD
METHOD ============================================
METHOD Comments from T0190.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0190
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 T0190.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 36
METHOD
METHOD ============================================
MODEL 1
A C 0.90
Q C 0.86
Q C 0.86
N C 0.86
I C 0.78
L C 0.52
S E 0.62
V E 0.80
H E 0.86
I E 0.85
L E 0.78
N E 0.62
Q C 0.50
Q C 0.67
T C 0.80
G C 0.86
K C 0.68
P C 0.60
A C 0.74
A C 0.81
D C 0.84
V C 0.64
T E 0.78
V E 0.90
T E 0.92
L E 0.92
E E 0.90
K E 0.87
K E 0.58
A C 0.78
D C 0.91
N C 0.89
G C 0.52
W E 0.72
L E 0.76
Q E 0.80
L E 0.77
N E 0.70
T E 0.65
A E 0.69
K E 0.71
T E 0.64
D C 0.85
K C 0.86
D C 0.91
G C 0.89
R C 0.66
I E 0.54
K C 0.72
A C 0.73
L C 0.71
W C 0.76
P C 0.79
E H 0.50
Q H 0.50
T C 0.50
A C 0.67
T C 0.68
T C 0.60
G E 0.50
D E 0.78
Y E 0.90
R E 0.92
V E 0.92
V E 0.90
F E 0.84
K E 0.60
T C 0.54
G H 0.76
D H 0.87
Y H 0.91
F H 0.92
K H 0.89
K H 0.77
Q C 0.67
N C 0.93
L C 0.91
E C 0.88
S C 0.77
F C 0.65
F C 0.59
P C 0.54
E C 0.50
I E 0.70
P E 0.86
V E 0.90
E E 0.92
F E 0.91
H E 0.88
I E 0.73
N C 0.54
K C 0.83
V C 0.87
N C 0.89
E C 0.77
H E 0.54
Y E 0.82
H E 0.86
V E 0.85
P E 0.81
L E 0.75
L E 0.77
L E 0.59
S C 0.71
Q C 0.74
Y C 0.70
G C 0.64
Y C 0.57
S C 0.53
T C 0.52
Y C 0.56
R C 0.71
G C 0.85
S C 0.91
END