PFRMAT SS
TARGET T0170
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0170.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0170.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0170.t2k.str.rdb  (weight 1.53983)
METHOD T0170.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 T0170.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0170
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 T0170.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 30
METHOD
METHOD ============================================
METHOD Comments from T0170.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0170
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 T0170.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 30
METHOD
METHOD ============================================
METHOD Comments from T0170.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0170
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 T0170.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 30
METHOD
METHOD ============================================
METHOD Comments from T0170.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0170
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 T0170.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 30
METHOD
METHOD ============================================
MODEL 1
Q C 0.86
P C 0.60
A H 0.57
K H 0.70
K H 0.73
T H 0.72
Y H 0.69
T H 0.68
W H 0.60
N H 0.52
T H 0.60
K H 0.90
E H 0.93
E H 0.94
A H 0.93
K H 0.95
Q H 0.95
A H 0.94
F H 0.94
K H 0.95
E H 0.95
L H 0.94
L H 0.92
K H 0.87
E H 0.73
K C 0.58
R C 0.89
V C 0.86
P C 0.90
S C 0.85
N C 0.91
A C 0.83
S C 0.76
W H 0.88
E H 0.90
Q H 0.91
A H 0.90
M H 0.91
K H 0.92
M H 0.91
I H 0.86
I H 0.72
N C 0.52
D C 0.83
P C 0.60
R C 0.52
Y H 0.51
S H 0.51
A H 0.45
L C 0.51
A C 0.72
N C 0.82
L H 0.69
S H 0.83
E H 0.88
K H 0.92
K H 0.93
Q H 0.93
A H 0.94
F H 0.95
N H 0.95
A H 0.95
Y H 0.94
K H 0.92
V H 0.89
Q H 0.80
T H 0.62
E C 0.62
K C 0.91
END