PFRMAT SS
TARGET T0492
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0492.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0492.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0492.t04.str2.rdb  (weight 1.54758)
METHOD T0492.t04.alpha.rdb  (weight 0.659012)
METHOD T0492.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0492.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0492.t2k.str2.rdb  (weight 1.54758)
METHOD T0492.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 T0492.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0492
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 T0492.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 61.0306
METHOD
METHOD ============================================
METHOD Comments from T0492.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0492
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 T0492.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 61.0306
METHOD
METHOD ============================================
METHOD Comments from T0492.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0492
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 T0492.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 61.0306
METHOD
METHOD ============================================
METHOD Comments from T0492.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0492
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 T0492.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 61.0306
METHOD
METHOD ============================================
METHOD Comments from T0492.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0492
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 T0492.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 347
METHOD
METHOD ============================================
METHOD Comments from T0492.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0492
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 T0492.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 347
METHOD
METHOD ============================================
METHOD Comments from T0492.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0492
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 T0492.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 347
METHOD
METHOD ============================================
METHOD Comments from T0492.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0492
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 T0492.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 347
METHOD
METHOD ============================================
MODEL 1
M C 0.90
F C 0.78
S C 0.73
L H 0.67
R H 0.69
D H 0.62
A C 0.70
K C 0.89
C C 0.87
G C 0.92
Q C 0.70
T E 0.81
V E 0.89
K E 0.91
V E 0.91
V E 0.86
K E 0.86
L E 0.73
H C 0.60
G C 0.86
T C 0.83
G H 0.57
A H 0.86
L H 0.93
K H 0.95
R H 0.95
R H 0.95
I H 0.95
M H 0.93
D H 0.88
M C 0.48
G C 0.89
I C 0.82
T C 0.85
R C 0.89
G C 0.91
C C 0.59
E E 0.86
I E 0.91
Y E 0.92
I E 0.91
R E 0.90
K E 0.89
V E 0.76
A C 0.52
P C 0.76
L C 0.88
G C 0.90
D C 0.85
P C 0.54
I E 0.87
Q E 0.92
I E 0.93
N E 0.93
V E 0.87
R C 0.70
G C 0.84
Y E 0.70
E E 0.88
L E 0.90
S E 0.89
L E 0.75
R C 0.52
K H 0.66
S H 0.71
A H 0.73
A H 0.66
E H 0.52
M C 0.42
I C 0.43
E E 0.61
V C 0.56
E C 0.91
END