PFRMAT SS
TARGET T0141
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0141.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0141.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0141.t2k.str.rdb  (weight 1.53983)
METHOD T0141.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 T0141.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0141
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 T0141.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 58
METHOD
METHOD ============================================
METHOD Comments from T0141.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0141
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 T0141.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 58
METHOD
METHOD ============================================
METHOD Comments from T0141.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0141
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 T0141.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 58
METHOD
METHOD ============================================
METHOD Comments from T0141.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0141
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 T0141.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 58
METHOD
METHOD ============================================
MODEL 1
M C 0.90
L C 0.73
L C 0.70
D C 0.73
E C 0.73
G C 0.75
W C 0.60
L C 0.48
A C 0.50
E C 0.61
A C 0.59
R C 0.63
R C 0.57
V C 0.73
P C 0.80
S C 0.84
P C 0.79
H C 0.79
Y C 0.70
D C 0.76
C C 0.76
R C 0.83
P C 0.79
D C 0.77
D C 0.76
E C 0.79
N C 0.75
P C 0.73
S C 0.50
L E 0.91
L E 0.93
V E 0.93
V E 0.91
H E 0.77
N C 0.60
I C 0.72
S C 0.82
L C 0.85
P C 0.83
P H 0.56
G H 0.72
E H 0.75
F H 0.75
G H 0.71
G H 0.71
P H 0.76
W H 0.80
I H 0.85
D H 0.86
A H 0.84
L H 0.79
F H 0.62
T C 0.52
G C 0.72
T C 0.77
I C 0.74
D C 0.85
P C 0.76
N C 0.78
A C 0.70
H C 0.73
P C 0.54
Y C 0.48
F H 0.42
A C 0.43
G C 0.52
I C 0.73
A C 0.77
H C 0.81
L C 0.75
R C 0.57
V E 0.70
S E 0.80
A E 0.87
H E 0.90
C E 0.91
L E 0.92
I E 0.90
R E 0.58
R C 0.85
D C 0.93
G C 0.87
E E 0.69
I E 0.91
V E 0.88
Q E 0.90
Y E 0.86
V E 0.73
P C 0.60
F H 0.54
D H 0.57
K H 0.62
R H 0.48
A H 0.41
W H 0.37
H C 0.36
A C 0.52
G C 0.66
V C 0.69
S C 0.66
S C 0.63
Y C 0.64
Q C 0.75
G C 0.81
R C 0.75
E C 0.69
R C 0.67
C C 0.65
N C 0.66
D C 0.69
F C 0.61
S E 0.58
I E 0.73
G E 0.82
I E 0.88
E E 0.88
L E 0.82
E E 0.64
G C 0.69
T C 0.85
D C 0.88
T C 0.85
L C 0.85
A C 0.86
Y C 0.87
T C 0.86
D H 0.94
A H 0.95
Q H 0.96
Y H 0.96
Q H 0.96
Q H 0.95
L H 0.96
A H 0.96
A H 0.96
V H 0.96
T H 0.96
N H 0.96
A H 0.96
L H 0.95
I H 0.93
T H 0.85
R H 0.66
Y C 0.70
P C 0.90
A C 0.88
I C 0.90
A H 0.72
N H 0.74
N H 0.72
M C 0.47
T C 0.53
G C 0.54
H C 0.55
C C 0.56
N C 0.59
I C 0.68
A C 0.84
P C 0.78
E C 0.77
R C 0.68
K C 0.63
T C 0.59
D C 0.78
P C 0.82
G C 0.82
P C 0.82
S C 0.86
F C 0.82
D C 0.80
W H 0.89
A H 0.93
R H 0.94
F H 0.94
R H 0.94
A H 0.89
L H 0.82
V H 0.55
T C 0.78
P C 0.83
S C 0.77
S C 0.72
H C 0.71
K C 0.59
E C 0.61
M C 0.73
T C 0.91
END