PFRMAT SS
TARGET T0139
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0139.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0139.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0139.t2k.str.rdb  (weight 1.53983)
METHOD T0139.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 T0139.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0139
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 T0139.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 3
METHOD
METHOD ============================================
METHOD Comments from T0139.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0139
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 T0139.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 3
METHOD
METHOD ============================================
METHOD Comments from T0139.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0139
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 T0139.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 3
METHOD
METHOD ============================================
METHOD Comments from T0139.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0139
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 T0139.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 3
METHOD
METHOD ============================================
MODEL 1
T C 0.82
G C 0.78
I C 0.66
S C 0.67
R C 0.48
E H 0.49
T H 0.55
S H 0.69
S H 0.76
D H 0.87
V H 0.88
A H 0.87
L H 0.86
A H 0.89
S H 0.89
H H 0.89
I H 0.90
L H 0.91
T H 0.90
A H 0.86
L H 0.77
R H 0.68
E C 0.52
K C 0.75
Q C 0.82
A C 0.84
P C 0.81
E C 0.60
L C 0.54
S C 0.54
L C 0.61
S C 0.67
S C 0.50
Q C 0.52
D C 0.51
L H 0.57
E H 0.58
L H 0.55
V C 0.51
T C 0.61
K C 0.59
E C 0.65
D C 0.82
P H 0.62
K H 0.68
A H 0.72
L H 0.74
A H 0.67
V H 0.59
A H 0.56
L H 0.45
N C 0.45
W C 0.50
D C 0.53
I H 0.50
K H 0.49
K H 0.54
T H 0.63
E H 0.76
T H 0.79
V H 0.87
Q H 0.88
E H 0.89
A H 0.86
C H 0.82
E H 0.87
R H 0.88
E H 0.89
L H 0.90
A H 0.89
L H 0.87
R H 0.85
L H 0.87
Q H 0.84
Q H 0.82
T H 0.74
Q H 0.72
S H 0.66
L H 0.64
H H 0.51
S C 0.57
L C 0.72
R C 0.91
END