PFRMAT SS
TARGET T0520
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0520.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0520.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0520.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 T0520.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 1499
METHOD
METHOD ============================================
METHOD Comments from T0520.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 1499
METHOD
METHOD ============================================
METHOD Comments from T0520.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0520
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 T0520.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 1499
METHOD
METHOD ============================================
MODEL 1
S C 0.96
N C 0.91
A C 0.86
E C 0.69
R C 0.51
R E 0.57
L E 0.70
C E 0.83
A E 0.84
I E 0.87
L E 0.78
A E 0.65
A E 0.48
D C 0.40
M H 0.53
A H 0.60
G H 0.54
Y H 0.64
S H 0.74
R H 0.83
L H 0.85
M H 0.83
E H 0.71
R C 0.50
N C 0.77
E C 0.92
T H 0.91
D H 0.95
V H 0.97
L H 0.97
N H 0.98
R H 0.97
Q H 0.97
K H 0.97
L H 0.97
Y H 0.96
R H 0.96
R H 0.96
E H 0.95
L H 0.95
I H 0.96
D H 0.97
P H 0.97
A H 0.97
I H 0.97
A H 0.94
Q H 0.80
A C 0.57
G C 0.96
G C 0.84
Q E 0.73
I E 0.90
V E 0.90
K E 0.87
T E 0.83
T E 0.66
G C 0.67
D C 0.70
G E 0.75
M E 0.82
L E 0.84
A E 0.82
R E 0.70
F C 0.65
D C 0.87
T C 0.90
A C 0.78
Q C 0.56
A H 0.53
A H 0.75
L H 0.88
R H 0.91
C H 0.94
A H 0.97
L H 0.97
E H 0.97
I H 0.97
Q H 0.98
Q H 0.97
A H 0.97
M H 0.96
Q H 0.95
Q H 0.92
R H 0.88
E H 0.85
E H 0.75
D H 0.64
T C 0.60
P C 0.74
R C 0.82
K C 0.88
E C 0.88
R C 0.78
I C 0.52
Q E 0.79
Y E 0.94
R E 0.95
I E 0.95
G E 0.89
I E 0.82
N E 0.64
I C 0.52
G C 0.61
D C 0.50
I E 0.68
V E 0.80
L E 0.73
E E 0.49
D C 0.64
G C 0.74
D C 0.76
I C 0.61
F C 0.63
G C 0.69
D H 0.73
A H 0.86
V H 0.95
N H 0.96
V H 0.97
A H 0.97
A H 0.97
R H 0.96
L H 0.95
E H 0.95
A H 0.88
I H 0.76
S C 0.50
E C 0.84
P C 0.89
G C 0.91
A C 0.54
I E 0.89
C E 0.91
V E 0.79
S C 0.68
D H 0.89
I H 0.94
V H 0.96
H H 0.96
Q H 0.94
I H 0.90
T H 0.75
Q H 0.60
D C 0.55
R C 0.62
V C 0.74
S C 0.79
E C 0.70
P C 0.56
F E 0.57
T E 0.60
D E 0.54
L C 0.59
G C 0.74
L C 0.54
Q E 0.75
K E 0.82
V E 0.69
K C 0.59
N C 0.83
I C 0.84
T C 0.86
R C 0.80
P C 0.68
I E 0.72
R E 0.92
V E 0.96
W E 0.96
Q E 0.94
W E 0.81
V C 0.59
P C 0.87
D C 0.88
A C 0.84
D C 0.80
R C 0.79
D C 0.81
Q C 0.86
S C 0.89
H C 0.91
D C 0.94
P C 0.93
Q C 0.92
P C 0.80
S C 0.75
H C 0.60
V C 0.60
Q C 0.73
H C 0.97
END