PFRMAT SS
TARGET YDR031W
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YDR031W.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YDR031W.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YDR031W.t2k.str2.rdb  (weight 1.54758)
METHOD YDR031W.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 YDR031W.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YDR031W
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 YDR031W.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 31
METHOD
METHOD ============================================
METHOD Comments from YDR031W.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YDR031W
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 YDR031W.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 31
METHOD
METHOD ============================================
METHOD Comments from YDR031W.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YDR031W
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.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 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment YDR031W.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 31
METHOD
METHOD ============================================
METHOD Comments from YDR031W.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YDR031W
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 YDR031W.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 31
METHOD
METHOD ============================================
MODEL 1
M C 0.81
S C 0.77
D C 0.58
I H 0.79
L H 0.88
D H 0.92
E H 0.94
I H 0.95
V H 0.95
I H 0.95
E H 0.95
D H 0.95
V H 0.95
V H 0.93
A H 0.83
N H 0.72
C C 0.52
P H 0.82
Q H 0.89
E H 0.90
F H 0.92
L H 0.91
Q H 0.88
Y H 0.81
H H 0.66
K H 0.67
C H 0.65
I H 0.60
R H 0.45
D C 0.67
N C 0.88
E C 0.80
E C 0.80
N C 0.79
P C 0.66
G C 0.50
K H 0.57
C H 0.58
K H 0.57
D H 0.61
G H 0.66
R H 0.65
M H 0.49
I H 0.50
L H 0.54
S H 0.54
T H 0.58
C H 0.55
I H 0.60
R H 0.60
E C 0.51
K C 0.68
V C 0.67
P H 0.50
S H 0.72
V H 0.90
K H 0.92
S H 0.92
I H 0.92
M H 0.91
S H 0.87
E H 0.75
C H 0.66
S H 0.73
E H 0.86
P H 0.88
M H 0.91
K H 0.94
K H 0.94
Y H 0.95
D H 0.95
Q H 0.96
C H 0.95
I H 0.94
R H 0.91
D H 0.79
N H 0.52
M H 0.51
G H 0.56
T H 0.55
R H 0.62
T H 0.64
I H 0.61
N H 0.63
E H 0.88
N H 0.91
C H 0.92
L H 0.94
G H 0.94
F H 0.94
L H 0.95
Q H 0.95
D H 0.95
L H 0.95
R H 0.94
K H 0.89
C H 0.78
A H 0.64
E H 0.51
L C 0.62
Q C 0.61
V C 0.60
K C 0.68
N C 0.76
K C 0.76
N C 0.83
I C 0.83
K C 0.88
P C 0.79
S C 0.75
I C 0.71
N C 0.80
G C 0.78
V C 0.68
N C 0.54
L E 0.44
E E 0.55
L E 0.56
I E 0.47
K C 0.61
D C 0.91
END