PFRMAT SS
TARGET T0602
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0602.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0602.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0602.t04.str2.rdb  (weight 1.54758)
METHOD T0602.t04.alpha.rdb  (weight 0.659012)
METHOD T0602.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0602.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0602.t2k.str2.rdb  (weight 1.54758)
METHOD T0602.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 T0602.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0602
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 T0602.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 64.8643
METHOD
METHOD ============================================
METHOD Comments from T0602.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0602
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 T0602.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 64.8643
METHOD
METHOD ============================================
METHOD Comments from T0602.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0602
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 T0602.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 64.8643
METHOD
METHOD ============================================
METHOD Comments from T0602.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0602
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 T0602.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 64.8643
METHOD
METHOD ============================================
METHOD Comments from T0602.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0602
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 T0602.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 75
METHOD
METHOD ============================================
METHOD Comments from T0602.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0602
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 T0602.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 75
METHOD
METHOD ============================================
METHOD Comments from T0602.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0602
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 T0602.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 75
METHOD
METHOD ============================================
METHOD Comments from T0602.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0602
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 T0602.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 75
METHOD
METHOD ============================================
MODEL 1
S C 0.78
N C 0.67
A C 0.67
M C 0.69
E C 0.70
R C 0.73
H H 0.61
Q H 0.85
H H 0.90
L H 0.93
L H 0.95
S H 0.95
E H 0.95
Y H 0.96
Q H 0.96
Q H 0.95
I H 0.95
L H 0.94
T H 0.90
L H 0.86
S H 0.87
E H 0.95
Q H 0.96
M H 0.96
L H 0.96
V H 0.96
L H 0.95
A H 0.92
T H 0.82
E H 0.48
G C 0.71
N C 0.67
W H 0.84
D H 0.94
A H 0.95
L H 0.96
V H 0.96
D H 0.95
L H 0.95
E H 0.95
M H 0.96
T H 0.96
Y H 0.96
L H 0.96
K H 0.96
A H 0.96
V H 0.96
E H 0.95
S H 0.94
T H 0.92
A H 0.86
N H 0.67
I C 0.59
T C 0.76
I C 0.78
S C 0.80
S C 0.79
C C 0.84
S C 0.84
S C 0.82
L H 0.89
M H 0.93
L H 0.93
Q H 0.94
D H 0.94
L H 0.93
L H 0.94
R H 0.95
E H 0.95
K H 0.95
L H 0.95
R H 0.96
A H 0.95
I H 0.94
L H 0.92
D H 0.84
N H 0.63
E H 0.91
I H 0.95
E H 0.95
I H 0.95
K H 0.95
R H 0.94
L H 0.92
L H 0.90
Q H 0.92
L H 0.92
R H 0.92
L H 0.95
D H 0.95
R H 0.94
L H 0.95
S H 0.95
D H 0.93
L H 0.90
V H 0.82
G H 0.56
Q H 0.55
S H 0.57
T H 0.69
K H 0.81
Q H 0.87
Q H 0.90
A H 0.90
V H 0.89
N H 0.85
N H 0.81
T H 0.71
Y H 0.54
G C 0.59
Q C 0.62
F C 0.73
P C 0.84
D C 0.87
H C 0.65
A E 0.54
L E 0.50
L C 0.68
L C 0.77
G C 0.85
E C 0.84
T C 0.86
Q C 0.91
END