PFRMAT SS
TARGET YGR030C
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YGR030C.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YGR030C.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YGR030C.t2k.str.rdb  (weight 1.53983)
METHOD YGR030C.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 YGR030C.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YGR030C
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 YGR030C.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 YGR030C.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YGR030C
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 YGR030C.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 YGR030C.t2k.str.rdb
METHOD ============================================
METHOD TARGET YGR030C
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 YGR030C.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 YGR030C.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YGR030C
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 YGR030C.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 0.89
I C 0.73
N C 0.69
G C 0.59
V C 0.41
Y E 0.51
Y E 0.36
N C 0.42
E C 0.39
I C 0.41
S C 0.44
R C 0.47
D C 0.52
L C 0.55
D C 0.61
I C 0.58
S C 0.64
S C 0.57
S H 0.49
T H 0.66
Q H 0.72
C H 0.76
L H 0.80
R H 0.78
F H 0.75
L H 0.68
K H 0.66
E H 0.63
T H 0.53
V H 0.42
I C 0.45
P H 0.52
S H 0.53
L H 0.50
A C 0.48
N C 0.63
N C 0.79
G C 0.84
N C 0.82
N C 0.79
S C 0.67
T C 0.52
S E 0.52
I E 0.63
Q E 0.64
Y E 0.59
H C 0.45
G C 0.52
I C 0.50
S C 0.60
K C 0.66
N C 0.70
D C 0.64
N C 0.55
I H 0.49
K H 0.54
K H 0.61
S H 0.58
V H 0.66
N H 0.63
K H 0.64
L H 0.65
D H 0.63
K H 0.66
Q H 0.62
I H 0.51
N C 0.46
M H 0.58
A H 0.58
D H 0.52
R H 0.49
S C 0.53
L C 0.61
G C 0.70
L C 0.56
Q C 0.43
Q E 0.63
V E 0.80
V E 0.83
C E 0.82
I E 0.77
F E 0.63
S C 0.50
Y C 0.72
G C 0.78
P C 0.53
H H 0.58
I H 0.80
Q H 0.84
K H 0.83
M H 0.86
L H 0.86
S H 0.86
I H 0.90
L H 0.90
E H 0.88
I H 0.82
F H 0.76
K H 0.67
K H 0.48
G C 0.66
Y C 0.57
I C 0.49
K C 0.59
N C 0.69
N C 0.71
K C 0.56
K E 0.41
I E 0.51
Y E 0.51
Q E 0.47
W C 0.38
N C 0.45
K C 0.46
L C 0.49
T C 0.49
S C 0.43
F C 0.40
D E 0.41
I C 0.40
K C 0.47
R C 0.49
E C 0.56
G C 0.65
R C 0.55
N C 0.49
E H 0.55
L H 0.56
Q H 0.59
E H 0.66
E H 0.60
R H 0.49
L C 0.53
K C 0.57
V C 0.61
P C 0.53
I E 0.74
L E 0.84
V E 0.85
T E 0.84
L E 0.78
V E 0.60
S C 0.61
D C 0.68
S C 0.59
E C 0.44
I E 0.41
I E 0.43
D E 0.44
L C 0.38
N C 0.47
L C 0.44
H C 0.47
S C 0.47
F C 0.53
T C 0.60
K C 0.75
Q C 0.92
END