PFRMAT SS
TARGET T0564
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0564.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0564.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0564.t04.str2.rdb  (weight 1.54758)
METHOD T0564.t04.alpha.rdb  (weight 0.659012)
METHOD T0564.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0564.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0564.t2k.str2.rdb  (weight 1.54758)
METHOD T0564.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 T0564.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0564
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 T0564.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 38.4637
METHOD
METHOD ============================================
METHOD Comments from T0564.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0564
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 T0564.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 38.4637
METHOD
METHOD ============================================
METHOD Comments from T0564.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0564
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 T0564.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 38.4637
METHOD
METHOD ============================================
METHOD Comments from T0564.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0564
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 T0564.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 38.4637
METHOD
METHOD ============================================
METHOD Comments from T0564.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0564
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 T0564.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 95
METHOD
METHOD ============================================
METHOD Comments from T0564.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0564
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 T0564.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 95
METHOD
METHOD ============================================
METHOD Comments from T0564.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0564
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 T0564.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 95
METHOD
METHOD ============================================
METHOD Comments from T0564.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0564
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 T0564.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 95
METHOD
METHOD ============================================
MODEL 1
M C 0.76
A C 0.68
P C 0.58
L E 0.51
Q E 0.69
Q E 0.79
K E 0.81
Q E 0.89
V E 0.90
V E 0.91
V E 0.91
S E 0.84
N E 0.75
K E 0.49
R C 0.47
E E 0.48
K C 0.58
P C 0.61
V C 0.80
N C 0.82
D C 0.84
R C 0.78
R C 0.78
S C 0.73
R C 0.74
Q C 0.67
Q C 0.68
E C 0.59
V C 0.47
S C 0.49
P C 0.58
A C 0.68
G C 0.77
T C 0.75
S C 0.65
M E 0.53
R E 0.76
Y E 0.87
E E 0.92
A E 0.93
S E 0.93
F E 0.92
K E 0.88
P E 0.83
L C 0.52
N C 0.76
G C 0.89
G C 0.86
L C 0.73
E E 0.71
K E 0.83
T E 0.89
F E 0.90
R E 0.90
L E 0.78
Q C 0.58
A H 0.54
Q H 0.59
Q H 0.62
Y H 0.53
H C 0.49
A C 0.48
L C 0.59
T C 0.81
V C 0.77
G C 0.82
D C 0.68
Q E 0.56
G E 0.72
T E 0.82
L E 0.87
S E 0.87
Y E 0.84
K E 0.68
G E 0.57
T E 0.58
R E 0.70
F E 0.75
V E 0.68
G E 0.58
F E 0.53
V C 0.59
S C 0.80
R C 0.86
T C 0.89
P C 0.85
D C 0.83
N C 0.83
E C 0.90
END