PFRMAT SS
TARGET T0590
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0590.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0590.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0590.t04.str2.rdb  (weight 1.54758)
METHOD T0590.t04.alpha.rdb  (weight 0.659012)
METHOD T0590.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0590.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0590.t2k.str2.rdb  (weight 1.54758)
METHOD T0590.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 T0590.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0590
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 T0590.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 1824
METHOD
METHOD ============================================
METHOD Comments from T0590.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0590
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 T0590.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 1824
METHOD
METHOD ============================================
METHOD Comments from T0590.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0590
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 T0590.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 1824
METHOD
METHOD ============================================
METHOD Comments from T0590.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0590
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 T0590.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 1824
METHOD
METHOD ============================================
METHOD Comments from T0590.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0590
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 T0590.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 1316
METHOD
METHOD ============================================
METHOD Comments from T0590.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0590
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 T0590.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 1316
METHOD
METHOD ============================================
METHOD Comments from T0590.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0590
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 T0590.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 1316
METHOD
METHOD ============================================
METHOD Comments from T0590.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0590
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 T0590.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 1316
METHOD
METHOD ============================================
MODEL 1
M C 0.88
N C 0.87
A C 0.84
R C 0.87
D C 0.84
N C 0.62
K E 0.59
F E 0.75
N E 0.82
T E 0.83
W E 0.83
N E 0.67
D C 0.57
S C 0.82
R C 0.87
G C 0.87
N C 0.76
Y C 0.71
W C 0.74
S C 0.74
D C 0.69
Y C 0.71
E C 0.65
G C 0.49
S E 0.66
D E 0.72
E E 0.68
N C 0.51
G C 0.70
D C 0.76
G C 0.65
I E 0.67
G E 0.86
D E 0.91
S E 0.92
A E 0.93
Y E 0.92
A E 0.92
V E 0.88
N E 0.68
P C 0.71
E C 0.82
A C 0.85
G C 0.81
S C 0.67
M E 0.52
D E 0.56
Y E 0.66
M E 0.73
P E 0.79
L E 0.84
M E 0.86
E E 0.88
Y E 0.87
L E 0.79
H E 0.59
S C 0.65
S C 0.78
P C 0.82
V C 0.82
L C 0.80
P C 0.64
T E 0.63
A E 0.75
R E 0.76
F E 0.78
T E 0.76
S E 0.66
D C 0.56
I C 0.70
T C 0.78
E C 0.78
G C 0.76
F C 0.65
A C 0.58
P C 0.55
L E 0.65
S E 0.80
V E 0.84
R E 0.86
F E 0.80
K E 0.63
D C 0.72
F C 0.82
S C 0.89
E C 0.88
N C 0.80
A E 0.57
T E 0.78
S E 0.87
R E 0.87
L E 0.88
W E 0.88
M E 0.78
F E 0.48
G C 0.79
D C 0.87
G C 0.88
N C 0.75
T C 0.68
S C 0.73
D C 0.75
S C 0.77
P C 0.73
S C 0.74
P C 0.68
L E 0.51
H E 0.77
T E 0.82
F E 0.78
F E 0.56
N C 0.67
E C 0.76
G C 0.66
E E 0.65
Y E 0.87
I E 0.91
V E 0.92
S E 0.93
L E 0.93
I E 0.92
V E 0.89
S E 0.74
N C 0.73
E C 0.85
N C 0.91
D C 0.89
S C 0.74
D E 0.54
S E 0.59
A E 0.76
S E 0.82
V E 0.81
T E 0.82
I E 0.76
R E 0.66
A C 0.89
END