PFRMAT SS
TARGET T0176
AUTHOR 4069-6308-1312
METHOD This file is the result of combining several RDB files, specifically
METHOD T0176.t2k.dssp-ebghstl.rdb (weight 1.53986)
METHOD T0176.t2k.stride-ebghtl.rdb (weight 1.24869)
METHOD T0176.t2k.str.rdb (weight 1.53983)
METHOD T0176.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 T0176.t2k.dssp-ebghstl.rdb
METHOD ============================================
METHOD TARGET T0176
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 T0176.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 31
METHOD
METHOD ============================================
METHOD Comments from T0176.t2k.stride-ebghtl.rdb
METHOD ============================================
METHOD TARGET T0176
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 T0176.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 31
METHOD
METHOD ============================================
METHOD Comments from T0176.t2k.str.rdb
METHOD ============================================
METHOD TARGET T0176
METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.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 str )
METHOD The input amino acid frequencies were determined from
METHOD alignment T0176.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 31
METHOD
METHOD ============================================
METHOD Comments from T0176.t2k.alpha.rdb
METHOD ============================================
METHOD TARGET T0176
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 T0176.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 31
METHOD
METHOD ============================================
MODEL 1
M C 0.87
D C 0.77
G C 0.71
V C 0.51
M H 0.47
S H 0.52
A H 0.48
V E 0.38
T E 0.55
V E 0.59
N C 0.48
D C 0.84
D C 0.91
G C 0.60
L E 0.83
V E 0.91
L E 0.93
R E 0.93
L E 0.92
Y E 0.91
I E 0.83
Q C 0.54
P C 0.79
K C 0.87
A C 0.75
S C 0.71
R C 0.60
D C 0.66
S C 0.62
I C 0.48
V C 0.49
G C 0.58
L C 0.69
H C 0.77
G C 0.79
D C 0.76
E E 0.61
V E 0.85
K E 0.90
V E 0.92
A E 0.90
I E 0.81
T E 0.55
A C 0.78
P C 0.90
P C 0.87
V C 0.77
D C 0.61
G H 0.49
Q H 0.80
A H 0.87
N H 0.92
S H 0.95
H H 0.96
L H 0.96
V H 0.96
K H 0.96
F H 0.96
L H 0.96
G H 0.96
K H 0.94
Q H 0.86
F H 0.48
R C 0.92
V C 0.90
A C 0.88
K C 0.50
S C 0.49
Q C 0.37
V E 0.73
V E 0.87
I E 0.86
E E 0.71
K C 0.60
G C 0.77
E C 0.71
L C 0.67
G C 0.70
R C 0.69
H C 0.61
K E 0.55
Q E 0.75
I E 0.85
K E 0.85
I E 0.67
I C 0.71
N C 0.89
P C 0.83
Q C 0.74
Q C 0.67
I C 0.75
P H 0.74
P H 0.90
E H 0.92
V H 0.92
A H 0.90
A H 0.85
L H 0.73
I C 0.53
N C 0.92
END