PFRMAT SS
TARGET T0396
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0396.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0396.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0396.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 T0396.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0396
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 T0396.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 141
METHOD
METHOD ============================================
METHOD Comments from T0396.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0396
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 T0396.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 141
METHOD
METHOD ============================================
METHOD Comments from T0396.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0396
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 T0396.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 141
METHOD
METHOD ============================================
MODEL 1
G C 0.95
S C 0.91
M H 0.65
L H 0.67
H H 0.74
W H 0.64
G H 0.63
P H 0.95
K H 0.97
Y H 0.97
W H 0.97
R H 0.97
S H 0.97
L H 0.97
H H 0.97
L H 0.97
Y H 0.96
A H 0.92
I H 0.79
F H 0.58
F C 0.84
S C 0.91
D C 0.92
A C 0.95
P C 0.96
S C 0.96
W H 0.84
K H 0.89
E H 0.93
K H 0.96
Y H 0.96
E H 0.96
A H 0.97
I H 0.97
Q H 0.97
W H 0.97
I H 0.97
L H 0.96
N H 0.92
F H 0.90
I H 0.83
E H 0.71
S H 0.64
L C 0.72
P C 0.84
C C 0.71
T H 0.87
R H 0.91
C H 0.93
Q H 0.96
H H 0.96
H H 0.95
A H 0.97
F H 0.97
S H 0.97
Y H 0.97
L H 0.95
T H 0.87
K H 0.69
N C 0.76
P C 0.94
L C 0.92
T C 0.84
L C 0.81
N C 0.87
N C 0.90
S H 0.89
E H 0.94
D H 0.96
F H 0.97
Q H 0.97
Y H 0.98
W H 0.97
T H 0.97
F H 0.97
A H 0.95
F H 0.91
H H 0.84
N H 0.85
N H 0.91
V H 0.95
N H 0.95
N H 0.94
R H 0.90
L H 0.56
N C 0.91
K C 0.94
K C 0.86
I C 0.75
I C 0.74
S C 0.79
W C 0.58
S H 0.57
E H 0.60
Y H 0.59
K H 0.62
N H 0.69
I H 0.71
Y H 0.63
E H 0.47
Q C 0.66
S C 0.84
I C 0.86
L C 0.89
K C 0.98
END