
PFRMAT SS
TARGET T0099
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0099
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-28687/target-align-28687.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 163.155
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0099
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.alpha.22620/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: Mon Jun 12 11:24:44 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-28687/target-align-28687.a2m
METHOD 
METHOD  guide seq name: T0099
METHOD ###end 0
MODEL 1
E E    0.438
F E    0.567
I E      0.6
A E    0.595
I E    0.563
Y E     0.52
D C    0.409
Y C    0.449
K C    0.579
A C    0.637
E C    0.668
T C    0.702
E C    0.644
E C    0.582
D C    0.483
L C    0.438
T C    0.424
I C    0.428
K C    0.592
K C    0.579
G C    0.637
E C    0.527
K E    0.579
L E    0.659
E E    0.679
I E    0.666
I E    0.595
E E    0.451
K C    0.561
E C    0.653
G C    0.633
D C    0.574
W E    0.438
W E    0.537
K E     0.55
A E    0.531
K E    0.518
A E     0.49
I C    0.392
G C    0.558
S C    0.634
G C    0.676
E C    0.553
I C    0.433
G C    0.483
Y C     0.46
I C    0.494
P C    0.607
A C    0.407
N H    0.391
Y H    0.422
I E    0.436
A E    0.434
A E    0.425
A C     0.55
E C    0.785
END


