PFRMAT SS
TARGET T0467
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0467.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0467.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0467.t04.str2.rdb  (weight 1.54758)
METHOD T0467.t04.alpha.rdb  (weight 0.659012)
METHOD T0467.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0467.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0467.t2k.str2.rdb  (weight 1.54758)
METHOD T0467.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 T0467.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0467
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	    7 (1 EBGHSTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0467.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 47.4357
METHOD
METHOD ============================================
METHOD Comments from T0467.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0467
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	    6 (1 EBGHTL )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0467.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 47.4357
METHOD
METHOD ============================================
METHOD Comments from T0467.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0467
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   13 (1 str2 )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0467.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 47.4357
METHOD
METHOD ============================================
METHOD Comments from T0467.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0467
METHOD Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net
METHOD This is a 4-layer network, with 
METHOD	window	units
METHOD	    3	   13
METHOD	    7	   13
METHOD	    9	   13
METHOD	   11	   11 (1 ABCDEFGHIST )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0467.t04-thin90.a2m.gz
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 1)
METHOD The weighting was determined by the posterior distribution
METHOD after regularizing with /projects/compbio/lib/recode3.20comp.
METHOD Counts were regularized to probabilities using
METHOD /projects/compbio/lib/recode3.20comp
METHOD Total sequence weight for alignment was 47.4357
METHOD
METHOD ============================================
METHOD Comments from T0467.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0467
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 T0467.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 86
METHOD
METHOD ============================================
METHOD Comments from T0467.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0467
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 T0467.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 86
METHOD
METHOD ============================================
METHOD Comments from T0467.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0467
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 T0467.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 86
METHOD
METHOD ============================================
METHOD Comments from T0467.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0467
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 T0467.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 86
METHOD
METHOD ============================================
MODEL 1
M C 0.81
D C 0.67
L C 0.53
N C 0.49
R C 0.50
M C 0.59
G C 0.72
K C 0.77
D C 0.65
E E 0.56
Y E 0.65
Y E 0.78
V E 0.87
Q E 0.89
I E 0.88
T E 0.73
V C 0.51
D C 0.63
G E 0.64
K E 0.83
E E 0.90
V E 0.88
H E 0.85
S E 0.63
K C 0.61
A C 0.75
D C 0.80
N C 0.81
G C 0.77
Q C 0.64
K C 0.56
Y E 0.52
K E 0.65
D E 0.78
Y E 0.86
E E 0.90
Y E 0.91
K E 0.90
L E 0.84
T E 0.81
G E 0.73
F E 0.79
D C 0.64
K C 0.85
D C 0.93
G C 0.91
K C 0.70
E E 0.85
K E 0.87
E E 0.92
L E 0.91
E E 0.91
F E 0.89
T E 0.72
A C 0.59
Q C 0.79
K C 0.81
N C 0.75
L C 0.71
R C 0.79
K C 0.76
E C 0.81
A C 0.51
F E 0.84
L E 0.90
R E 0.92
V E 0.92
Y E 0.91
H E 0.84
S C 0.59
D C 0.84
K C 0.77
K C 0.63
G C 0.51
V E 0.73
S E 0.77
A E 0.69
W H 0.35
E H 0.35
E E 0.36
V C 0.62
K C 0.74
K H 0.70
D H 0.67
E H 0.58
L C 0.63
P C 0.66
A H 0.92
K H 0.93
V H 0.95
K H 0.94
E H 0.90
K H 0.81
L H 0.47
G C 0.72
V C 0.82
K C 0.91
END