PFRMAT SS
TARGET T0136
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0136.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0136.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0136.t2k.str.rdb  (weight 1.53983)
METHOD T0136.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 T0136.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0136
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 T0136.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 72
METHOD
METHOD ============================================
METHOD Comments from T0136.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0136
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 T0136.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 72
METHOD
METHOD ============================================
METHOD Comments from T0136.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0136
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 T0136.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 72
METHOD
METHOD ============================================
METHOD Comments from T0136.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0136
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 T0136.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 72
METHOD
METHOD ============================================
MODEL 1
A C 0.89
E C 0.80
N H 0.56
N H 0.62
N H 0.66
L H 0.71
K H 0.70
L H 0.65
A H 0.87
S H 0.92
T H 0.92
M H 0.94
E H 0.95
G H 0.95
R H 0.95
V H 0.96
E H 0.96
Q H 0.95
L H 0.95
A H 0.96
E H 0.95
Q H 0.95
R H 0.95
Q H 0.95
V H 0.94
I H 0.92
E H 0.84
A H 0.58
G C 0.73
G C 0.79
G C 0.68
E H 0.93
R H 0.95
R H 0.95
V H 0.95
E H 0.94
K H 0.92
Q H 0.89
H H 0.88
S H 0.82
Q C 0.56
G C 0.88
K C 0.86
Q C 0.73
T C 0.83
A H 0.90
R H 0.94
E H 0.95
R H 0.95
L H 0.94
N H 0.92
N H 0.86
L H 0.76
L H 0.53
D C 0.85
P C 0.84
H C 0.89
S C 0.79
F C 0.38
D H 0.48
E H 0.55
V H 0.78
G H 0.83
A H 0.90
F H 0.87
R H 0.84
K H 0.71
H H 0.61
R C 0.50
T C 0.55
T C 0.66
L C 0.72
F C 0.72
G C 0.77
M C 0.65
D C 0.60
K C 0.54
A C 0.61
V C 0.70
V C 0.91
END