PFRMAT SS
TARGET T0389
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0389.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0389.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0389.t2k.str.rdb  (weight 1.53983)
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 T0389.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 408
METHOD
METHOD ============================================
METHOD Comments from T0389.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 408
METHOD
METHOD ============================================
METHOD Comments from T0389.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0389
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 T0389.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 408
METHOD
METHOD ============================================
MODEL 1
M C 0.95
I C 0.72
G C 0.62
T C 0.55
Q C 0.50
I H 0.46
V H 0.48
T H 0.87
E H 0.91
R H 0.92
L H 0.93
V H 0.93
A H 0.91
L H 0.90
L H 0.86
E H 0.79
S H 0.60
G C 0.77
T C 0.87
E C 0.91
K C 0.84
V E 0.74
L E 0.96
L E 0.97
I E 0.96
D E 0.89
S E 0.50
R C 0.84
P C 0.92
F H 0.59
V H 0.77
E H 0.82
Y H 0.81
N H 0.70
T H 0.52
S C 0.68
H C 0.75
I C 0.78
L C 0.74
E C 0.76
A C 0.64
I E 0.59
N E 0.62
I C 0.57
N C 0.83
C H 0.53
S H 0.74
K H 0.83
L H 0.86
M H 0.83
K H 0.77
R H 0.69
R H 0.68
L H 0.60
Q H 0.53
Q C 0.59
D C 0.67
K C 0.53
V H 0.47
L H 0.50
I H 0.55
T H 0.53
E H 0.50
L H 0.42
I C 0.46
Q C 0.61
H C 0.49
S H 0.53
A H 0.58
K H 0.57
H H 0.52
K H 0.49
V C 0.45
D C 0.56
I C 0.65
D C 0.75
C C 0.81
S C 0.88
Q C 0.75
K E 0.66
V E 0.94
V E 0.97
V E 0.96
Y E 0.92
D E 0.50
Q C 0.90
S C 0.92
S C 0.86
Q C 0.80
D C 0.68
V C 0.59
A C 0.57
S H 0.50
L H 0.51
S H 0.51
S H 0.64
D H 0.67
C H 0.78
F H 0.92
L H 0.94
T H 0.95
V H 0.96
L H 0.96
L H 0.96
G H 0.95
K H 0.94
L H 0.90
E H 0.78
K C 0.62
S C 0.91
F C 0.91
N C 0.83
S C 0.58
V E 0.84
H E 0.94
L E 0.93
L E 0.79
A C 0.55
G C 0.80
G C 0.70
F H 0.79
A H 0.94
E H 0.96
F H 0.96
S H 0.96
R H 0.91
C H 0.81
F C 0.64
P C 0.50
G H 0.53
L H 0.56
C C 0.56
E C 0.69
G C 0.84
K C 0.87
S C 0.82
T C 0.77
L C 0.81
V C 0.81
P C 0.84
T C 0.85
C C 0.84
I C 0.86
S C 0.87
Q C 0.89
P C 0.89
A C 0.88
H C 0.85
H C 0.86
H C 0.84
H C 0.84
H C 0.88
H C 0.98
END