PFRMAT SS
TARGET T0181
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0181.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0181.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0181.t2k.str.rdb  (weight 1.53983)
METHOD T0181.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 T0181.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0181
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 T0181.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 2
METHOD
METHOD ============================================
METHOD Comments from T0181.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0181
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 T0181.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 2
METHOD
METHOD ============================================
METHOD Comments from T0181.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0181
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 T0181.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 2
METHOD
METHOD ============================================
METHOD Comments from T0181.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0181
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 T0181.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 2
METHOD
METHOD ============================================
MODEL 1
M C 0.90
S C 0.78
T C 0.68
V C 0.56
T E 0.54
K E 0.71
Y E 0.76
F E 0.77
Y E 0.71
K C 0.52
G C 0.73
E C 0.80
N C 0.81
T C 0.61
D E 0.62
L E 0.89
I E 0.91
V E 0.91
F E 0.87
A E 0.66
A C 0.68
S C 0.85
E C 0.73
E H 0.51
L H 0.62
V H 0.74
D H 0.77
E H 0.76
Y H 0.69
L H 0.52
K C 0.58
N C 0.84
P C 0.76
S C 0.73
I C 0.64
G C 0.64
K C 0.50
L H 0.71
S H 0.77
E H 0.71
V H 0.66
V H 0.50
E H 0.41
L E 0.45
F E 0.65
E E 0.73
V E 0.76
F E 0.75
T E 0.54
P C 0.68
Q C 0.81
D C 0.86
G C 0.86
R C 0.81
G C 0.82
A C 0.77
E C 0.65
G C 0.59
E C 0.46
L H 0.35
G H 0.37
A H 0.45
A H 0.49
S H 0.48
K H 0.83
A H 0.84
Q H 0.86
V H 0.84
E H 0.81
N H 0.74
E H 0.66
F C 0.50
G C 0.74
K C 0.71
G C 0.64
K C 0.52
K H 0.45
I H 0.82
E H 0.90
E H 0.91
V H 0.93
I H 0.94
D H 0.94
L H 0.94
I H 0.94
L H 0.91
R H 0.78
N C 0.61
G C 0.90
K C 0.87
P C 0.80
N C 0.82
S C 0.76
T C 0.68
T C 0.57
S C 0.53
S C 0.49
L C 0.42
K C 0.45
T C 0.54
K C 0.71
G C 0.80
G C 0.80
N C 0.73
A C 0.65
G C 0.66
T C 0.56
K C 0.50
A C 0.54
Y C 0.72
N C 0.92
END