
PFRMAT SS
TARGET T0097
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0097
METHOD  Using neural net overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net
METHOD  This is a 4-layer network, with 
METHOD 	window	units
METHOD 	    5	    9
METHOD 	    7	   10
METHOD 	    5	    9
METHOD 	   11	    3 (1 EHL2 )
METHOD  The input amino acid frequencies were determined from
METHOD  alignment /projects/compbio/tmp/hmm-target99-alpha-16392/target-align-16392.a2m
METHOD  with weighted counts, using EntropyWeight(1.4 bits/column, 10)
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 9.56816
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0097
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.alpha.28183/model.mod
METHOD  database_files: /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/bin/scripts/hmm-target99-dir/pcc/data/overrep-2260.verify.mixed.2d
METHOD  scoring_mode: local
METHOD  null_model: reverse
METHOD  scoring_algorithm: EM
METHOD  adjust_score: 2
METHOD  date: Fri Jun  9 01:10:23 2000
METHOD Method 2:
METHOD ###begin 0
METHOD 
METHOD  Protein secondary structure prediction by universal HMM
METHOD  HMM file: /projects/compbio/bin/scripts/hmm-target99-dir/pcc/scripts/gdac.test.initreest.38state.abb.isites.gd.updated.ghmm-128reest-1-128-105-0.07gd
METHOD  Alignment file: /projects/compbio/tmp/hmm-target99-alpha-16392/target-align-16392.a2m
METHOD 
METHOD  guide seq name: T0097
METHOD ###end 0
MODEL 1
G C     0.65
C C    0.538
L H     0.47
P H    0.588
A H    0.638
Y H    0.751
D H    0.765
A H    0.802
L H    0.802
A H    0.805
G H    0.804
Q H    0.791
F H    0.759
I H     0.74
E H    0.679
A H    0.567
S C    0.523
S H    0.522
R H    0.796
E H    0.802
A H    0.807
R H     0.83
Q H    0.838
A H    0.833
I H     0.83
L H    0.832
K H    0.836
Q H    0.815
G H    0.791
Q H    0.788
D H    0.768
G H    0.698
L H     0.64
S H    0.578
G H    0.549
V H    0.482
K C    0.474
E H    0.562
T H    0.596
D H     0.71
K H     0.74
K H    0.772
W H    0.765
A H    0.782
S H    0.792
Q H    0.788
Y H    0.781
L H    0.792
K H    0.796
I H    0.788
M H    0.787
G H    0.791
K H    0.788
I H    0.768
L H    0.749
D H    0.698
Q H    0.699
G H    0.549
E H     0.62
D H    0.637
F H    0.661
P H    0.701
A H     0.77
S H    0.816
E H     0.83
L H    0.852
A H    0.859
R H    0.854
I H    0.835
S H    0.823
K H    0.818
L H    0.785
I H    0.746
E H    0.638
N C    0.471
K C    0.554
M C    0.559
S C    0.629
E C     0.47
G C    0.495
K C    0.481
K H    0.695
E H    0.733
E H    0.759
L H    0.739
Q H    0.717
R H    0.709
S H    0.708
L H    0.675
N H      0.5
I H    0.601
L H     0.64
T H    0.648
A H    0.624
F H    0.568
R H    0.485
K C    0.461
K C    0.551
G C    0.612
A C    0.548
E C    0.499
K C    0.481
E C    0.502
E C    0.541
L C    0.687
END


