PFRMAT SS
TARGET T0161
AUTHOR 4069-6308-1312 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0161.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0161.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0161.t2k.str.rdb  (weight 1.53983)
METHOD T0161.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 T0161.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0161
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 T0161.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 T0161.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0161
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 T0161.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 T0161.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0161
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 T0161.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 T0161.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0161
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 T0161.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 0.88
S C 0.79
E H 0.49
T H 0.59
D H 0.66
L H 0.71
L H 0.74
L H 0.77
K H 0.75
M H 0.69
V H 0.58
R H 0.47
Q C 0.58
P C 0.58
V C 0.46
K C 0.36
L H 0.44
Y H 0.48
S H 0.46
V H 0.68
A H 0.72
T H 0.73
L H 0.74
F H 0.75
H H 0.77
E H 0.75
F H 0.81
S H 0.84
E H 0.84
V H 0.85
I H 0.82
T H 0.79
K H 0.74
L H 0.68
E H 0.63
H H 0.55
S H 0.48
V C 0.45
Q C 0.54
K C 0.58
E C 0.71
P C 0.68
T C 0.58
S C 0.50
L C 0.45
L C 0.51
S C 0.60
E H 0.52
E H 0.58
N H 0.57
W H 0.68
H H 0.77
K H 0.85
Q H 0.85
F H 0.86
L H 0.87
K H 0.85
F H 0.86
A H 0.82
Q H 0.74
A H 0.61
L C 0.59
P C 0.66
A C 0.61
H C 0.69
G C 0.76
S C 0.69
A C 0.52
S C 0.47
W H 0.41
L C 0.47
N C 0.59
L H 0.49
D H 0.62
D H 0.76
A H 0.83
L H 0.83
Q H 0.84
A H 0.81
V H 0.76
V H 0.61
G C 0.53
N C 0.61
S C 0.49
R H 0.68
S H 0.77
A H 0.84
F H 0.85
L H 0.89
H H 0.91
Q H 0.91
L H 0.92
I H 0.91
A H 0.89
K H 0.84
L H 0.74
K H 0.67
S H 0.59
R H 0.51
H C 0.43
L C 0.37
Q E 0.36
V E 0.50
L E 0.50
E E 0.49
L C 0.34
N C 0.49
K C 0.56
I C 0.66
G C 0.78
S C 0.78
E C 0.78
P C 0.71
L C 0.68
D C 0.68
L C 0.53
S C 0.60
N C 0.69
L C 0.80
P C 0.79
A C 0.74
P C 0.61
F E 0.47
Y E 0.65
V E 0.70
L E 0.63
L C 0.58
P C 0.63
E H 0.52
S H 0.57
F H 0.63
A H 0.66
A H 0.65
R H 0.61
I H 0.53
T H 0.53
L H 0.45
L E 0.42
V H 0.39
Q C 0.41
D C 0.54
K C 0.59
A C 0.62
L C 0.68
P C 0.60
Y E 0.49
V E 0.67
R E 0.75
V E 0.72
S E 0.65
F E 0.56
E E 0.49
Y E 0.44
W C 0.48
H C 0.72
A C 0.92
END