PFRMAT SS
TARGET T0188
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0188.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0188.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0188.t2k.str.rdb  (weight 1.53983)
METHOD T0188.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 T0188.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0188
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 T0188.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 38
METHOD
METHOD ============================================
METHOD Comments from T0188.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0188
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 T0188.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 38
METHOD
METHOD ============================================
METHOD Comments from T0188.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0188
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 T0188.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 38
METHOD
METHOD ============================================
METHOD Comments from T0188.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0188
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 T0188.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 38
METHOD
METHOD ============================================
MODEL 1
M C 0.86
I E 0.65
I E 0.86
A E 0.87
I E 0.85
P E 0.71
V C 0.61
S C 0.80
E C 0.87
N C 0.84
R C 0.82
G C 0.84
K C 0.78
D C 0.80
S C 0.73
P C 0.59
I C 0.52
S C 0.57
E C 0.54
H C 0.54
F C 0.54
G C 0.67
R C 0.69
A C 0.74
P C 0.80
Y E 0.55
F E 0.88
A E 0.92
F E 0.93
V E 0.91
K E 0.90
V E 0.68
K C 0.76
N C 0.90
N C 0.89
A E 0.50
I E 0.85
A E 0.86
D E 0.89
I E 0.84
S E 0.82
V E 0.79
E E 0.69
E E 0.50
N C 0.73
P C 0.76
L C 0.61
A C 0.55
Q C 0.61
D C 0.69
H C 0.78
V C 0.76
H C 0.73
G C 0.57
A C 0.45
V H 0.86
P H 0.92
N H 0.93
F H 0.94
V H 0.94
K H 0.92
E H 0.85
K C 0.61
G C 0.93
A C 0.88
E C 0.57
L E 0.93
V E 0.93
I E 0.93
V E 0.85
R C 0.61
G C 0.78
I C 0.77
G C 0.87
R H 0.61
R H 0.74
A H 0.93
I H 0.95
A H 0.95
A H 0.96
F H 0.95
E H 0.94
A H 0.90
M C 0.64
G C 0.94
V C 0.87
K E 0.64
V E 0.89
I E 0.89
K E 0.86
G C 0.50
A C 0.84
S C 0.90
G C 0.85
T C 0.74
V H 0.90
E H 0.94
E H 0.95
V H 0.95
V H 0.95
N H 0.95
Q H 0.94
Y H 0.92
L H 0.79
S C 0.59
G C 0.81
Q C 0.77
L C 0.64
K C 0.62
D C 0.48
S C 0.57
D C 0.64
Y C 0.73
E C 0.74
V C 0.74
H C 0.77
D C 0.79
H C 0.80
H C 0.81
H C 0.78
H C 0.78
E C 0.76
H C 0.79
H C 0.92
END