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 30
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 30
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 30
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 30
METHOD
METHOD ============================================
MODEL 1
G C 0.91
P C 0.85
A C 0.70
W C 0.78
P C 0.85
D C 0.86
S C 0.69
S C 0.70
T C 0.70
S H 0.78
E H 0.83
D H 0.87
A H 0.95
L H 0.96
K H 0.96
V H 0.96
L H 0.96
E H 0.94
K H 0.87
Y H 0.52
G C 0.88
I C 0.87
E C 0.81
T C 0.87
S C 0.87
E H 0.73
S H 0.78
V H 0.82
K H 0.79
R H 0.73
A H 0.66
I H 0.53
L C 0.56
Q C 0.75
E C 0.82
T C 0.85
P C 0.78
K C 0.66
H C 0.64
L C 0.62
S C 0.66
N C 0.67
V E 0.50
E E 0.65
I E 0.86
H E 0.91
L E 0.92
I E 0.88
G E 0.61
N C 0.77
V C 0.55
Q H 0.83
K H 0.91
V H 0.93
C H 0.95
D H 0.96
E H 0.96
A H 0.96
K H 0.96
S H 0.95
L H 0.95
A H 0.95
K H 0.94
E H 0.88
K C 0.57
G C 0.94
F C 0.90
N C 0.69
A E 0.85
E E 0.91
I E 0.92
I E 0.85
T E 0.48
T C 0.64
S C 0.57
L C 0.51
D H 0.46
C H 0.53
E H 0.71
A H 0.91
R H 0.92
E H 0.93
A H 0.93
G H 0.95
R H 0.96
F H 0.95
I H 0.96
A H 0.96
S H 0.96
I H 0.96
M H 0.95
K H 0.95
E H 0.95
V H 0.94
K H 0.91
F H 0.82
K C 0.56
D C 0.92
R C 0.90
P C 0.84
L C 0.84
K C 0.89
K C 0.88
P C 0.68
A E 0.85
A E 0.92
L E 0.93
I E 0.87
F E 0.65
G C 0.77
G C 0.85
E C 0.65
T E 0.57
V E 0.75
V E 0.87
H E 0.89
V E 0.79
K E 0.56
G C 0.69
N C 0.83
G C 0.84
I C 0.85
G C 0.87
G C 0.79
R C 0.50
N H 0.71
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 0.84
E H 0.55
G C 0.77
I C 0.86
E C 0.86
G C 0.88
V E 0.49
I E 0.80
L E 0.89
C E 0.84
S E 0.69
A C 0.62
G C 0.83
T C 0.92
END