PFRMAT SS
TARGET T0187
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0187.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0187.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0187.t2k.str.rdb  (weight 1.53983)
METHOD T0187.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 T0187.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0187
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 T0187.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 29
METHOD
METHOD ============================================
METHOD Comments from T0187.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0187
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 T0187.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 29
METHOD
METHOD ============================================
METHOD Comments from T0187.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0187
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 T0187.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 29
METHOD
METHOD ============================================
METHOD Comments from T0187.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0187
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 T0187.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 29
METHOD
METHOD ============================================
MODEL 1
L C 0.91
K C 0.89
K C 0.88
P C 0.64
A E 0.85
A E 0.92
L E 0.92
I E 0.86
F E 0.56
G C 0.82
G C 0.87
E C 0.66
T E 0.56
V E 0.74
V E 0.87
H E 0.89
V E 0.79
K E 0.55
G C 0.70
N C 0.83
G C 0.84
I C 0.85
G C 0.87
G C 0.79
R C 0.49
N H 0.72
Q H 0.92
E H 0.94
L H 0.95
A H 0.96
L H 0.96
S H 0.95
A H 0.95
A H 0.95
I H 0.94
A H 0.90
L H 0.83
E H 0.55
G C 0.77
I C 0.86
E C 0.85
G C 0.88
V E 0.54
I E 0.83
L E 0.91
C E 0.90
S E 0.85
A E 0.65
G C 0.62
T C 0.74
D C 0.78
G C 0.82
T C 0.79
D C 0.80
G C 0.85
P C 0.74
T C 0.66
D C 0.56
A C 0.52
A C 0.64
G C 0.64
G E 0.57
I E 0.73
V E 0.54
D C 0.78
G C 0.50
S H 0.63
T H 0.80
A H 0.94
K H 0.94
T H 0.95
L H 0.94
K H 0.93
A H 0.82
M C 0.61
G C 0.90
E C 0.90
D C 0.86
P H 0.89
Y H 0.93
Q H 0.94
Y H 0.93
L H 0.87
K H 0.72
N H 0.57
N C 0.64
D C 0.69
S H 0.74
Y H 0.92
N H 0.94
A H 0.94
L H 0.94
K H 0.92
K H 0.81
S H 0.59
G C 0.60
A C 0.62
L C 0.37
L E 0.59
I E 0.59
T C 0.48
G C 0.83
P C 0.85
T C 0.84
G C 0.83
T C 0.77
N C 0.63
V C 0.54
N C 0.55
D E 0.52
L E 0.71
I E 0.78
I E 0.83
G E 0.85
L E 0.81
I E 0.67
V C 0.89
END