PFRMAT SS
TARGET T0388
AUTHOR SAM-T06-server 
METHOD This file is the result of combining several RDB files, specifically
METHOD T0388.t04.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0388.t04.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0388.t04.str2.rdb  (weight 1.54758)
METHOD T0388.t04.alpha.rdb  (weight 0.659012)
METHOD T0388.t2k.dssp-ebghstl.rdb  (weight 1.53986)
METHOD T0388.t2k.stride-ebghtl.rdb  (weight 1.24869)
METHOD T0388.t2k.str2.rdb  (weight 1.54758)
METHOD T0388.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 T0388.t04.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0388
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 T0388.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 2152
METHOD
METHOD ============================================
METHOD Comments from T0388.t04.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0388
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 T0388.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 2152
METHOD
METHOD ============================================
METHOD Comments from T0388.t04.str2.rdb
METHOD ============================================
METHOD TARGET T0388
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 T0388.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 2152
METHOD
METHOD ============================================
METHOD Comments from T0388.t04.alpha.rdb
METHOD ============================================
METHOD TARGET T0388
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 T0388.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 2152
METHOD
METHOD ============================================
METHOD Comments from T0388.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0388
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 T0388.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 960
METHOD
METHOD ============================================
METHOD Comments from T0388.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0388
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 T0388.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 960
METHOD
METHOD ============================================
METHOD Comments from T0388.t2k.str2.rdb
METHOD ============================================
METHOD TARGET T0388
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 T0388.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 960
METHOD
METHOD ============================================
METHOD Comments from T0388.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0388
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 T0388.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 960
METHOD
METHOD ============================================
MODEL 1
E C 0.60
N C 0.53
L E 0.42
Y E 0.60
F E 0.68
Q E 0.59
S C 0.48
M C 0.62
I C 0.71
N C 0.71
S C 0.69
F C 0.67
Y C 0.68
A C 0.57
F E 0.56
E E 0.75
V E 0.80
K E 0.82
D C 0.59
A C 0.83
K C 0.93
G C 0.93
R C 0.72
T E 0.82
V E 0.77
S E 0.58
L H 0.70
E H 0.73
K H 0.71
Y C 0.55
K C 0.82
G C 0.86
K C 0.65
V E 0.63
S E 0.88
L E 0.93
V E 0.92
V E 0.86
N E 0.63
V C 0.60
A C 0.58
S C 0.60
D C 0.70
C C 0.81
Q C 0.84
L C 0.82
T C 0.83
D H 0.71
R H 0.69
N H 0.73
Y H 0.75
L H 0.89
G H 0.91
L H 0.95
K H 0.95
E H 0.96
L H 0.95
H H 0.94
K H 0.93
E H 0.89
F H 0.76
G H 0.52
P C 0.59
S C 0.81
H C 0.89
F C 0.53
S E 0.89
V E 0.92
L E 0.91
A E 0.90
F E 0.82
P E 0.64
C C 0.65
N C 0.78
Q C 0.78
F C 0.81
G C 0.82
E C 0.83
S C 0.74
E C 0.82
P C 0.82
R C 0.83
P C 0.83
S H 0.75
K H 0.92
E H 0.94
V H 0.94
E H 0.95
S H 0.95
F H 0.95
A H 0.94
R H 0.93
K H 0.88
N H 0.74
Y C 0.67
G C 0.90
V C 0.86
T C 0.81
F C 0.62
P C 0.48
I E 0.48
F E 0.53
H C 0.45
K C 0.53
I C 0.51
K C 0.56
I C 0.63
L C 0.73
G C 0.71
S C 0.63
E C 0.62
G C 0.61
E C 0.53
P H 0.89
A H 0.93
F H 0.95
R H 0.95
F H 0.95
L H 0.94
V H 0.90
D H 0.79
S H 0.55
S C 0.76
K C 0.79
K C 0.77
E C 0.78
P C 0.68
R C 0.54
W E 0.49
N C 0.62
F C 0.58
W E 0.57
K E 0.81
Y E 0.87
L E 0.88
V E 0.86
N C 0.76
P C 0.87
E C 0.93
G C 0.89
Q C 0.70
V E 0.88
V E 0.85
K E 0.85
F E 0.78
W E 0.63
R C 0.64
P C 0.84
E C 0.84
E C 0.83
P C 0.89
I H 0.77
E H 0.80
V H 0.82
I H 0.85
R H 0.92
P H 0.93
D H 0.94
I H 0.95
A H 0.95
A H 0.95
L H 0.93
V H 0.92
R H 0.90
Q H 0.84
V H 0.80
I H 0.76
I H 0.72
K H 0.54
K H 0.48
K H 0.52
E C 0.53
D C 0.63
L C 0.85
END