PFRMAT SS
TARGET T0132
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0132.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0132.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0132.t2k.str.rdb  (weight 1.53983)
METHOD T0132.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 T0132.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0132
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 T0132.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 89
METHOD
METHOD ============================================
METHOD Comments from T0132.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0132
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 T0132.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 89
METHOD
METHOD ============================================
METHOD Comments from T0132.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0132
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 T0132.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 89
METHOD
METHOD ============================================
METHOD Comments from T0132.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0132
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 T0132.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 89
METHOD
METHOD ============================================
MODEL 1
M C 0.90
S C 0.77
A C 0.71
N C 0.71
F C 0.75
T C 0.79
D C 0.77
K C 0.75
N C 0.59
G C 0.52
R C 0.50
Q C 0.67
S C 0.74
K C 0.81
G C 0.78
V E 0.65
L E 0.87
L E 0.89
L E 0.91
R E 0.89
T E 0.85
L E 0.80
A E 0.66
M C 0.61
P C 0.65
S C 0.59
D C 0.55
T C 0.68
N C 0.79
A C 0.70
N C 0.73
G C 0.67
D C 0.38
I H 0.42
F H 0.54
G H 0.73
G H 0.83
W H 0.95
I H 0.95
M H 0.95
S H 0.95
Q H 0.94
M H 0.95
D H 0.95
M H 0.96
G H 0.96
G H 0.96
A H 0.96
I H 0.96
L H 0.96
A H 0.96
K H 0.95
E H 0.90
I H 0.79
A C 0.56
H C 0.85
G C 0.88
R C 0.72
V E 0.66
V E 0.86
T E 0.91
V E 0.88
A E 0.85
V E 0.71
E C 0.48
S E 0.45
M E 0.78
N E 0.81
F E 0.80
I E 0.72
K E 0.56
P E 0.56
I E 0.59
S C 0.60
V C 0.79
G C 0.90
D C 0.70
V E 0.81
V E 0.92
C E 0.93
C E 0.92
Y E 0.90
G E 0.90
Q E 0.91
C E 0.91
L E 0.86
K E 0.84
V E 0.55
G C 0.69
R C 0.68
S E 0.56
S E 0.82
I E 0.91
K E 0.93
I E 0.92
K E 0.93
V E 0.93
E E 0.93
V E 0.91
W E 0.88
V E 0.75
K E 0.47
K C 0.57
V C 0.56
A C 0.63
S C 0.71
E C 0.79
P C 0.79
I C 0.76
G C 0.75
E C 0.53
R E 0.56
Y E 0.70
C E 0.78
V E 0.79
T E 0.82
D E 0.88
A E 0.90
V E 0.92
F E 0.93
T E 0.92
F E 0.92
V E 0.90
A E 0.84
V E 0.77
D C 0.77
N C 0.86
N C 0.93
G C 0.92
R C 0.81
S E 0.59
R C 0.60
T C 0.66
I C 0.77
P C 0.81
R C 0.83
E C 0.82
N C 0.74
N C 0.78
Q C 0.82
E C 0.88
L C 0.89
E H 0.90
K H 0.92
A H 0.94
L H 0.94
A H 0.93
L H 0.92
I H 0.87
S H 0.81
E H 0.66
Q C 0.54
P C 0.67
L C 0.90
END