PFRMAT SS
TARGET YCL046W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YCL046W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YCL046W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YCL046W.t2k.str.rdb  (weight 1.53983)
METHOD YCL046W.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 YCL046W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YCL046W
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 YCL046W.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 YCL046W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YCL046W
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 YCL046W.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 YCL046W.t2k.str.rdb
METHOD ============================================
METHOD TARGET YCL046W
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 YCL046W.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 YCL046W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YCL046W
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 YCL046W.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
V C 0.76
K C 0.74
G C 0.69
K C 0.52
T H 0.44
F H 0.52
L H 0.56
K H 0.56
R H 0.50
I C 0.49
C C 0.77
P C 0.70
E C 0.55
E C 0.51
T C 0.54
L C 0.58
N C 0.65
E C 0.52
E C 0.50
T C 0.48
K C 0.45
Q C 0.42
E C 0.36
V C 0.36
S C 0.40
V C 0.43
G C 0.54
F H 0.50
D H 0.59
K H 0.66
M H 0.72
R H 0.73
T H 0.72
L H 0.70
L H 0.63
R H 0.55
S H 0.46
R C 0.48
E C 0.53
S C 0.65
G C 0.79
M C 0.66
T C 0.49
F C 0.52
S C 0.63
Q C 0.72
G C 0.79
P C 0.69
K C 0.55
L C 0.43
A C 0.43
S C 0.43
C C 0.40
Q H 0.42
S H 0.42
V H 0.41
I C 0.37
N C 0.52
A C 0.53
S C 0.58
S C 0.56
E C 0.51
K H 0.49
T H 0.49
A H 0.56
W H 0.60
T H 0.60
Q H 0.59
L H 0.55
V H 0.50
F H 0.43
R H 0.38
K H 0.46
S C 0.47
K C 0.50
M C 0.51
K C 0.49
T C 0.46
Y C 0.46
T C 0.48
K C 0.48
S E 0.49
V E 0.70
H E 0.82
V E 0.90
I E 0.90
F E 0.89
I E 0.85
A E 0.75
M C 0.48
G C 0.70
E C 0.75
G C 0.77
E C 0.72
D C 0.70
E C 0.59
S C 0.53
V C 0.47
D C 0.45
M C 0.42
N C 0.47
V C 0.47
G C 0.53
I C 0.53
S C 0.69
Y C 0.92
END