PFRMAT SS
TARGET YBR224W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YBR224W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YBR224W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YBR224W.t2k.str.rdb  (weight 1.53983)
METHOD YBR224W.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 YBR224W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YBR224W
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 YBR224W.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 1
METHOD
METHOD ============================================
METHOD Comments from YBR224W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YBR224W
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 YBR224W.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 1
METHOD
METHOD ============================================
METHOD Comments from YBR224W.t2k.str.rdb
METHOD ============================================
METHOD TARGET YBR224W
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 YBR224W.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 1
METHOD
METHOD ============================================
METHOD Comments from YBR224W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YBR224W
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 YBR224W.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 1
METHOD
METHOD ============================================
MODEL 1
M C 0.87
I C 0.63
F C 0.55
D C 0.54
S C 0.49
L C 0.45
T C 0.43
M C 0.43
T C 0.49
Q H 0.51
S H 0.53
S H 0.57
L H 0.63
S H 0.64
L H 0.63
L H 0.58
L H 0.55
L H 0.55
T H 0.53
G C 0.49
A H 0.44
I H 0.43
F H 0.44
S H 0.44
I H 0.73
S H 0.77
A H 0.83
L H 0.81
Y H 0.78
L H 0.78
T H 0.76
L H 0.76
F H 0.70
H H 0.65
R H 0.56
C H 0.46
A H 0.41
T C 0.43
F C 0.46
S C 0.52
A C 0.52
T C 0.54
S C 0.53
D C 0.52
L E 0.39
F E 0.59
L E 0.66
L E 0.66
V E 0.55
P E 0.49
L E 0.39
K E 0.39
F E 0.40
V C 0.38
S C 0.46
R C 0.47
D C 0.54
I H 0.52
N H 0.50
D H 0.53
R H 0.57
L H 0.54
K H 0.49
T H 0.45
H C 0.43
Y C 0.47
H C 0.53
H C 0.51
S C 0.54
C C 0.60
L C 0.69
G C 0.80
S C 0.78
P H 0.46
F H 0.57
L H 0.56
C H 0.57
I H 0.61
I H 0.65
F H 0.67
L H 0.64
F H 0.58
I H 0.52
S H 0.50
P H 0.66
L H 0.68
L H 0.66
N H 0.55
Y H 0.54
H H 0.48
F H 0.53
R H 0.54
S H 0.50
L C 0.45
V C 0.60
R C 0.76
P C 0.80
P C 0.69
K C 0.56
I C 0.50
H C 0.57
Q C 0.59
K C 0.69
G C 0.78
S C 0.74
I C 0.66
P C 0.64
T C 0.51
L C 0.44
T C 0.50
K C 0.49
N C 0.59
A H 0.46
E H 0.51
T H 0.52
R H 0.49
C H 0.48
S H 0.56
H H 0.64
H H 0.63
L H 0.70
K H 0.72
Q H 0.71
A H 0.66
A H 0.57
A C 0.48
T C 0.65
G C 0.78
E C 0.64
V E 0.56
C E 0.65
K E 0.78
V E 0.89
V E 0.90
V E 0.91
I E 0.89
I E 0.81
K C 0.46
G C 0.65
H C 0.49
I E 0.44
L C 0.41
K C 0.52
D C 0.59
C C 0.51
S C 0.38
I E 0.57
F E 0.52
F E 0.53
F E 0.50
I H 0.42
I H 0.48
F H 0.44
P H 0.53
L H 0.47
I H 0.43
Y C 0.40
P H 0.50
L H 0.53
F H 0.46
I H 0.43
N C 0.41
C C 0.53
S C 0.57
S C 0.55
K C 0.53
Y C 0.60
N C 0.70
G C 0.75
L C 0.80
Q C 0.92
END