PFRMAT SS
TARGET T0135
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0135.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0135.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0135.t2k.str.rdb  (weight 1.53983)
METHOD T0135.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 T0135.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0135
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 T0135.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 14
METHOD
METHOD ============================================
METHOD Comments from T0135.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0135
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 T0135.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 14
METHOD
METHOD ============================================
METHOD Comments from T0135.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0135
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 T0135.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 14
METHOD
METHOD ============================================
METHOD Comments from T0135.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0135
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 T0135.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 14
METHOD
METHOD ============================================
MODEL 1
M C 0.90
A C 0.81
T C 0.79
R C 0.79
T C 0.74
P C 0.71
K C 0.66
L C 0.45
V E 0.54
K E 0.71
H E 0.90
T E 0.91
L E 0.92
L E 0.91
T E 0.87
R E 0.80
F E 0.56
K C 0.72
D C 0.74
E C 0.82
I C 0.86
T C 0.89
R H 0.83
E H 0.89
Q H 0.93
I H 0.95
D H 0.95
N H 0.95
Y H 0.95
I H 0.94
N H 0.90
D H 0.86
Y H 0.87
T H 0.87
N H 0.83
L H 0.85
L H 0.81
D H 0.66
L H 0.59
I C 0.65
P C 0.65
S C 0.55
M E 0.61
K E 0.73
S E 0.78
F E 0.71
N E 0.60
W C 0.60
G C 0.74
T C 0.73
D C 0.73
L C 0.74
G C 0.77
M C 0.56
E C 0.54
S C 0.53
A H 0.63
E H 0.67
L H 0.66
N C 0.49
R C 0.73
G C 0.85
Y C 0.79
T C 0.62
H E 0.85
A E 0.92
F E 0.92
E E 0.90
S E 0.79
T E 0.64
F C 0.61
E C 0.81
S C 0.89
K H 0.81
S H 0.87
G H 0.90
L H 0.94
Q H 0.93
E H 0.90
Y H 0.89
L H 0.78
D H 0.61
S C 0.77
A H 0.78
A H 0.79
L H 0.84
A H 0.81
A H 0.74
F H 0.74
A H 0.73
E H 0.66
G H 0.60
F H 0.46
L H 0.44
P H 0.56
T H 0.53
L H 0.46
S C 0.62
Q C 0.76
R C 0.58
L E 0.75
V E 0.87
I E 0.86
D E 0.76
Y E 0.50
F C 0.50
L C 0.64
Y C 0.92
END