PFRMAT SS
TARGET T0138
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0138.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0138.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0138.t2k.str.rdb  (weight 1.53983)
METHOD T0138.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 T0138.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0138
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 T0138.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 T0138.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0138
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 T0138.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 T0138.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0138
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 T0138.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 T0138.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0138
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 T0138.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
M C 0.91
L C 0.84
S C 0.80
Q C 0.61
I E 0.47
A E 0.64
I E 0.72
C E 0.73
I E 0.68
W E 0.60
V C 0.47
E C 0.73
S C 0.70
T H 0.76
A H 0.84
I H 0.88
L H 0.90
Q H 0.90
D H 0.90
C H 0.90
Q H 0.90
R H 0.87
A H 0.81
L H 0.67
S H 0.54
A C 0.52
D C 0.61
R H 0.72
Y H 0.71
Q H 0.74
L H 0.65
Q H 0.60
V H 0.61
C H 0.58
E H 0.57
S H 0.57
G H 0.83
E H 0.90
M H 0.91
L H 0.93
L H 0.94
E H 0.93
Y H 0.92
A H 0.89
Q H 0.81
T H 0.62
H C 0.65
R C 0.50
D C 0.59
Q C 0.53
I C 0.58
D E 0.50
C E 0.87
L E 0.89
I E 0.90
L E 0.87
V E 0.75
A C 0.50
A C 0.76
N C 0.78
P C 0.73
S C 0.64
F H 0.76
R H 0.92
A H 0.94
V H 0.95
V H 0.95
Q H 0.95
Q H 0.94
L H 0.91
C H 0.85
F H 0.67
E C 0.65
G C 0.81
V C 0.64
V E 0.68
V E 0.73
P E 0.80
A E 0.89
I E 0.91
V E 0.90
V E 0.81
G E 0.52
D C 0.78
R C 0.85
D C 0.78
S C 0.79
E C 0.82
D C 0.85
P C 0.82
D C 0.83
E C 0.85
P C 0.84
A C 0.83
K C 0.79
E C 0.80
Q C 0.69
L C 0.48
Y E 0.67
H E 0.72
S E 0.75
A E 0.80
E E 0.86
L E 0.86
H E 0.84
L E 0.59
G C 0.72
I H 0.64
H H 0.71
Q H 0.79
L H 0.86
E H 0.82
Q H 0.74
L H 0.59
P H 0.80
Y H 0.90
Q H 0.92
V H 0.95
D H 0.96
A H 0.96
A H 0.95
L H 0.95
A H 0.95
E H 0.92
F H 0.91
L H 0.85
R H 0.75
L H 0.63
A C 0.62
P C 0.59
V C 0.46
E C 0.49
T C 0.57
M C 0.75
A C 0.92
END