PFRMAT SS
TARGET B
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YCR024C-B.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YCR024C-B.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YCR024C-B.t2k.str2.rdb  (weight 1.54758)
METHOD YCR024C-B.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 YCR024C-B.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YCR024C-B
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 YCR024C-B.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 YCR024C-B.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YCR024C-B
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 YCR024C-B.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 YCR024C-B.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YCR024C-B
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 YCR024C-B.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 YCR024C-B.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YCR024C-B
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 YCR024C-B.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 0.85
C C 0.61
V C 0.50
C C 0.47
A C 0.45
I C 0.53
P C 0.47
F H 0.53
F H 0.63
E H 0.65
F H 0.62
F H 0.54
L H 0.48
P C 0.48
F C 0.50
I C 0.60
P C 0.51
H H 0.49
Y H 0.57
A H 0.52
F E 0.44
L E 0.58
L E 0.63
F E 0.67
V E 0.64
S E 0.52
S E 0.54
V E 0.66
R E 0.73
F E 0.73
T E 0.67
V E 0.50
N C 0.61
E C 0.55
R C 0.45
C E 0.49
Y E 0.60
Y E 0.71
L E 0.77
V E 0.77
C E 0.75
V E 0.68
L E 0.56
K E 0.46
L H 0.44
N H 0.47
C H 0.68
A H 0.80
F H 0.83
F H 0.83
F H 0.79
M H 0.78
V H 0.74
M H 0.71
I H 0.72
F H 0.71
E H 0.65
L H 0.66
K H 0.64
R H 0.59
V H 0.52
C H 0.42
V H 0.42
S H 0.42
Y H 0.40
L C 0.46
D C 0.58
R C 0.56
S C 0.61
R C 0.59
K C 0.49
I E 0.54
Q E 0.65
I E 0.69
V E 0.60
S E 0.52
F E 0.44
F C 0.53
P C 0.49
F E 0.57
I E 0.70
T E 0.73
I E 0.81
I E 0.78
F E 0.71
F E 0.51
H C 0.74
S C 0.92
END