PFRMAT SS
TARGET T0632
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0632.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0632.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0632.t04.str2.rdb  (weight 1.54758)
METHOD T0632.t04.alpha.rdb  (weight 0.659012)
METHOD T0632.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0632.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0632.t2k.str2.rdb  (weight 1.54758)
METHOD T0632.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 T0632.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0632
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 T0632.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 2067
METHOD
METHOD ============================================
METHOD Comments from T0632.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0632
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 T0632.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 2067
METHOD
METHOD ============================================
METHOD Comments from T0632.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0632
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 T0632.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 2067
METHOD
METHOD ============================================
METHOD Comments from T0632.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0632
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 T0632.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 2067
METHOD
METHOD ============================================
METHOD Comments from T0632.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0632
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 T0632.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 1934
METHOD
METHOD ============================================
METHOD Comments from T0632.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0632
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 T0632.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 1934
METHOD
METHOD ============================================
METHOD Comments from T0632.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0632
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 T0632.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 1934
METHOD
METHOD ============================================
METHOD Comments from T0632.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0632
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 T0632.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 1934
METHOD
METHOD ============================================
MODEL 1
M C 0.84
D C 0.54
K H 0.55
R H 0.61
L H 0.54
Q C 0.55
Q C 0.61
D C 0.68
R H 0.54
I H 0.68
V H 0.73
D H 0.72
K H 0.71
M H 0.67
E H 0.57
R C 0.53
F C 0.80
L C 0.65
S C 0.59
T H 0.51
A H 0.55
N H 0.51
E H 0.51
E C 0.47
E H 0.57
K H 0.60
D C 0.49
V C 0.63
L C 0.83
S C 0.86
S H 0.56
I H 0.69
V H 0.71
D H 0.77
G H 0.84
L H 0.85
L H 0.83
A H 0.83
K H 0.80
Q H 0.68
E H 0.51
R C 0.49
R C 0.57
Y C 0.66
A C 0.72
T C 0.67
Y C 0.53
L H 0.54
A H 0.57
S H 0.51
L C 0.48
T C 0.69
Q C 0.77
I E 0.62
E E 0.85
S E 0.90
Q E 0.88
E E 0.88
R E 0.73
E C 0.58
D C 0.91
G C 0.91
R E 0.72
F E 0.91
E E 0.93
V E 0.92
R E 0.91
L E 0.80
P E 0.55
I C 0.72
G C 0.86
P C 0.50
L H 0.56
V H 0.58
N C 0.57
N C 0.78
P C 0.78
L C 0.69
N C 0.63
M H 0.42
V H 0.53
H H 0.69
G H 0.82
G H 0.92
I H 0.95
T H 0.96
A H 0.96
T H 0.95
L H 0.96
L H 0.95
D H 0.95
T H 0.95
A H 0.94
M H 0.94
G H 0.94
Q H 0.93
M H 0.93
V H 0.90
N H 0.84
R H 0.68
Q C 0.51
L C 0.81
P C 0.87
D C 0.86
G C 0.89
Q C 0.76
S E 0.56
A E 0.80
V E 0.85
T E 0.87
S E 0.87
E E 0.91
L E 0.90
N E 0.91
I E 0.89
H E 0.86
Y E 0.86
V E 0.77
K E 0.72
P E 0.58
G C 0.67
M C 0.83
G C 0.91
T C 0.82
Y E 0.69
L E 0.90
R E 0.92
A E 0.92
V E 0.92
A E 0.90
S E 0.90
I E 0.91
V E 0.84
H E 0.79
Q C 0.59
G C 0.79
K C 0.70
Q E 0.71
R E 0.90
I E 0.92
V E 0.93
V E 0.92
E E 0.93
G E 0.91
K E 0.92
V E 0.91
Y E 0.87
T C 0.56
D C 0.87
Q C 0.94
G C 0.89
E C 0.53
T E 0.91
V E 0.89
A E 0.93
M E 0.92
G E 0.92
T E 0.92
G E 0.91
S E 0.92
F E 0.91
F E 0.90
V E 0.87
L E 0.64
R C 0.64
S C 0.82
R C 0.88
G C 0.92
END