PFRMAT SS
TARGET T0630
AUTHOR SAM-T02-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0630.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0630.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0630.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 T0630.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0630
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 T0630.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 224
METHOD
METHOD ============================================
METHOD Comments from T0630.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0630
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 T0630.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 224
METHOD
METHOD ============================================
METHOD Comments from T0630.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0630
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 T0630.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 224
METHOD
METHOD ============================================
MODEL 1
M C 0.96
R C 0.83
A C 0.79
P C 0.78
I C 0.70
P C 0.79
E C 0.86
P C 0.93
K C 0.93
P C 0.89
G C 0.90
D C 0.75
L E 0.88
I E 0.95
E E 0.95
I E 0.83
F E 0.53
R C 0.68
P C 0.80
F C 0.70
Y C 0.51
R E 0.64
H E 0.85
W E 0.90
A E 0.96
I E 0.97
Y E 0.96
V E 0.81
G C 0.63
D C 0.93
G C 0.88
Y E 0.68
V E 0.92
V E 0.95
H E 0.93
L E 0.79
A E 0.53
P C 0.77
P C 0.82
S C 0.74
E C 0.66
V C 0.58
A C 0.52
G C 0.49
A C 0.48
G C 0.52
A C 0.41
A E 0.41
S E 0.43
V E 0.39
M E 0.35
S H 0.36
A H 0.44
L H 0.42
T C 0.45
D C 0.59
K C 0.58
A C 0.46
I E 0.40
V E 0.54
K E 0.55
K E 0.47
E E 0.39
L C 0.35
L H 0.36
Y H 0.39
D H 0.40
V H 0.41
A C 0.47
G C 0.67
S C 0.78
D C 0.69
K C 0.57
Y E 0.43
Q E 0.51
V E 0.49
N C 0.59
N C 0.64
K C 0.53
H C 0.48
D C 0.55
D C 0.61
K C 0.69
Y C 0.79
S C 0.88
P C 0.92
L C 0.91
P C 0.90
C H 0.52
S H 0.79
K H 0.92
I H 0.95
I H 0.96
Q H 0.97
R H 0.97
A H 0.97
E H 0.96
E H 0.93
L H 0.84
V H 0.66
G C 0.70
Q C 0.86
E C 0.82
V C 0.73
L C 0.67
Y C 0.45
K C 0.38
L E 0.38
T E 0.37
S H 0.40
E C 0.48
N C 0.54
C H 0.61
E H 0.80
H H 0.80
F H 0.91
V H 0.94
N H 0.93
E H 0.93
L H 0.90
R H 0.84
Y H 0.50
G C 0.88
V C 0.88
A C 0.78
R C 0.66
S C 0.63
D C 0.56
Q C 0.59
V C 0.64
R C 0.78
D C 0.98
END