PFRMAT SS
TARGET T0140
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0140.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0140.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0140.t2k.str.rdb  (weight 1.53983)
METHOD T0140.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 T0140.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0140
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 T0140.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 341
METHOD
METHOD ============================================
METHOD Comments from T0140.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0140
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 T0140.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 341
METHOD
METHOD ============================================
METHOD Comments from T0140.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0140
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 T0140.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 341
METHOD
METHOD ============================================
METHOD Comments from T0140.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0140
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 T0140.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 341
METHOD
METHOD ============================================
MODEL 1
M C 0.91
R C 0.71
G C 0.66
S C 0.60
H C 0.50
H C 0.49
H C 0.56
H C 0.72
H C 0.83
H C 0.61
G C 0.53
S C 0.44
R E 0.44
L E 0.46
Q C 0.52
S C 0.67
G C 0.62
K C 0.49
M E 0.67
T E 0.75
G E 0.86
I E 0.91
V E 0.92
K E 0.89
W E 0.87
F E 0.79
N E 0.76
A E 0.59
D C 0.46
K C 0.63
G C 0.71
F C 0.56
G E 0.69
F E 0.83
I E 0.81
T E 0.56
P C 0.64
D C 0.74
D C 0.75
G C 0.82
S C 0.61
K E 0.78
D E 0.85
V E 0.87
F E 0.86
V E 0.84
H E 0.76
F E 0.60
S C 0.44
A C 0.60
G C 0.67
S C 0.72
S C 0.49
G H 0.69
A H 0.76
A H 0.75
V H 0.70
R H 0.65
G H 0.54
N C 0.55
P C 0.77
Q C 0.86
Q C 0.87
G C 0.90
D C 0.57
R E 0.83
V E 0.89
E E 0.88
G E 0.87
K E 0.89
I E 0.92
K E 0.87
S E 0.90
I E 0.81
T E 0.64
D C 0.52
F C 0.67
G E 0.55
I E 0.79
F E 0.91
I E 0.90
G E 0.89
L E 0.68
D C 0.68
G C 0.88
G C 0.89
I C 0.61
D E 0.50
G E 0.73
L E 0.86
V E 0.85
H E 0.78
L H 0.39
S H 0.48
D H 0.60
I H 0.51
S C 0.52
W C 0.53
A C 0.53
Q C 0.49
A C 0.56
E C 0.74
A C 0.90
END