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
M C 0.91
F C 0.83
D C 0.84
P C 0.65
E H 0.58
S H 0.62
L H 0.83
K H 0.88
K H 0.92
L H 0.93
A H 0.94
I H 0.95
E H 0.95
I H 0.95
V H 0.96
K H 0.96
K H 0.95
S H 0.94
I H 0.91
E H 0.84
A H 0.66
V C 0.64
F C 0.86
P H 0.70
D H 0.86
R H 0.91
A H 0.91
V H 0.88
K H 0.82
E H 0.64
T C 0.49
L C 0.78
P C 0.80
K C 0.75
L C 0.82
N C 0.80
L C 0.87
D C 0.86
R C 0.65
V E 0.76
I E 0.92
L E 0.93
V E 0.89
A E 0.82
V C 0.51
G C 0.68
K H 0.69
A H 0.81
A H 0.89
W H 0.94
R H 0.94
M H 0.95
A H 0.95
K H 0.96
A H 0.95
A H 0.96
Y H 0.95
E H 0.93
V H 0.86
L H 0.69
G C 0.50
K C 0.63
K C 0.60
I C 0.62
R C 0.69
K C 0.73
G E 0.57
V E 0.88
V E 0.91
V E 0.89
T E 0.73
K C 0.61
Y C 0.85
G C 0.87
H C 0.80
S C 0.78
E C 0.77
G C 0.79
P C 0.76
I C 0.80
D C 0.80
D C 0.59
F E 0.67
E E 0.85
I E 0.90
Y E 0.85
E E 0.76
A C 0.52
G C 0.77
H C 0.87
P C 0.82
V C 0.83
P C 0.87
D C 0.83
E H 0.76
N H 0.81
T H 0.92
I H 0.96
K H 0.96
T H 0.96
T H 0.96
R H 0.96
R H 0.96
V H 0.96
L H 0.95
E H 0.95
L H 0.91
V H 0.86
D H 0.67
Q C 0.71
L C 0.88
N C 0.93
E C 0.72
N C 0.82
D C 0.71
T E 0.79
V E 0.92
L E 0.93
F E 0.93
L E 0.89
L E 0.71
S C 0.57
G C 0.80
G C 0.73
G C 0.51
S H 0.49
S H 0.48
L C 0.48
F C 0.61
E C 0.59
L C 0.69
P C 0.76
L C 0.68
E C 0.81
G C 0.87
V C 0.79
S C 0.87
L H 0.90
E H 0.94
E H 0.95
I H 0.95
Q H 0.95
K H 0.94
L H 0.93
T H 0.92
S H 0.91
A H 0.88
L H 0.79
L H 0.53
K C 0.86
END