PFRMAT SS
TARGET A
AUTHOR SAM-T02 
METHOD This file is the result of combining several RDB files, specifically
METHOD YBR221W-A.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD YBR221W-A.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD YBR221W-A.t2k.str2.rdb  (weight 1.54758)
METHOD YBR221W-A.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 YBR221W-A.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET YBR221W-A
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 YBR221W-A.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 YBR221W-A.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET YBR221W-A
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 YBR221W-A.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 YBR221W-A.t2k.str2.rdb
METHOD ============================================
METHOD TARGET YBR221W-A
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 YBR221W-A.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 YBR221W-A.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET YBR221W-A
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 YBR221W-A.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
F C 0.71
S C 0.61
H C 0.52
F C 0.46
E E 0.51
V C 0.53
S C 0.68
E C 0.75
N C 0.82
R C 0.83
P C 0.79
R C 0.72
K C 0.73
Q C 0.79
P C 0.72
R C 0.61
R C 0.55
K C 0.52
R C 0.46
I C 0.43
S C 0.44
L C 0.42
G C 0.48
M E 0.39
I E 0.53
N E 0.51
T E 0.56
V E 0.64
V E 0.62
S E 0.56
L C 0.60
D C 0.81
R C 0.92
END