PFRMAT SS
TARGET T0471
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0471.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0471.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0471.t04.str2.rdb  (weight 1.54758)
METHOD T0471.t04.alpha.rdb  (weight 0.659012)
METHOD T0471.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0471.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0471.t2k.str2.rdb  (weight 1.54758)
METHOD T0471.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 T0471.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0471
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 T0471.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 13.2224
METHOD
METHOD ============================================
METHOD Comments from T0471.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0471
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 T0471.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 13.2224
METHOD
METHOD ============================================
METHOD Comments from T0471.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0471
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 T0471.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 13.2224
METHOD
METHOD ============================================
METHOD Comments from T0471.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0471
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 T0471.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 13.2224
METHOD
METHOD ============================================
METHOD Comments from T0471.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0471
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 T0471.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 24
METHOD
METHOD ============================================
METHOD Comments from T0471.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0471
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 T0471.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 24
METHOD
METHOD ============================================
METHOD Comments from T0471.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0471
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 T0471.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 24
METHOD
METHOD ============================================
METHOD Comments from T0471.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0471
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 T0471.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 24
METHOD
METHOD ============================================
MODEL 1
M C 0.85
W C 0.64
N C 0.53
D H 0.77
L H 0.84
A H 0.84
V H 0.82
Y H 0.79
I H 0.78
I H 0.76
R H 0.73
C H 0.66
S C 0.43
G C 0.78
P C 0.85
G C 0.85
T C 0.69
R E 0.65
V E 0.90
V E 0.91
E E 0.91
V E 0.84
G E 0.70
A C 0.54
G C 0.77
R C 0.77
F C 0.74
L H 0.70
Y H 0.83
V H 0.93
S H 0.95
D H 0.95
Y H 0.95
I H 0.95
R H 0.93
K H 0.86
H C 0.58
S C 0.93
K C 0.89
V E 0.55
D E 0.84
L E 0.91
V E 0.91
L E 0.86
T E 0.73
D E 0.51
I C 0.59
K C 0.76
P C 0.82
S C 0.83
H C 0.83
G C 0.72
G C 0.53
I E 0.70
V E 0.73
R E 0.68
D E 0.46
D C 0.59
I C 0.64
T C 0.73
S C 0.86
P C 0.80
R C 0.76
M H 0.58
E H 0.66
I H 0.69
Y H 0.53
R C 0.51
G C 0.73
A C 0.73
A C 0.62
L E 0.84
I E 0.86
Y E 0.85
S E 0.71
I C 0.64
R C 0.86
P C 0.89
P C 0.66
A H 0.72
E H 0.76
I H 0.67
H H 0.69
S H 0.82
S H 0.90
L H 0.94
M H 0.95
R H 0.95
V H 0.94
A H 0.93
D H 0.85
A H 0.72
V C 0.59
G C 0.91
A C 0.88
R C 0.74
L E 0.90
I E 0.92
I E 0.92
K E 0.83
P C 0.55
L C 0.83
T C 0.83
G C 0.83
E C 0.75
D C 0.64
I C 0.63
V C 0.62
T C 0.63
E C 0.66
R C 0.59
K E 0.54
M E 0.65
K E 0.66
L E 0.61
V C 0.58
N C 0.77
Y C 0.72
G C 0.53
R E 0.72
T E 0.83
Y E 0.89
F E 0.89
Y E 0.88
E E 0.83
Y E 0.77
I E 0.62
A E 0.48
E C 0.51
V C 0.57
R C 0.70
S C 0.80
R C 0.92
END