
PFRMAT SS
TARGET T0102
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0102
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-6631/target-align-6631.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 1.95347
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0102
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.alpha.20073/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 16 10:53:43 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-6631/target-align-6631.a2m
METHOD 
METHOD  guide seq name: T0102
METHOD ###end 0
MODEL 1
M C    0.568
A H    0.513
K H    0.555
E H    0.579
F H    0.482
G C    0.698
I C    0.731
P C    0.652
A H    0.414
A H    0.484
V H    0.445
A H    0.433
G H    0.386
T H    0.386
V H    0.413
L E    0.438
N E    0.436
V E    0.451
V E    0.436
E H     0.37
A C    0.436
G C    0.616
G C    0.615
W E    0.416
V E    0.485
T E    0.472
T E    0.499
I E    0.526
V E    0.503
S E    0.474
I E     0.48
L E    0.457
T E    0.433
A E    0.415
V C     0.39
G C    0.579
S C    0.609
G C     0.59
G C    0.501
L H    0.495
S H    0.533
L H    0.598
L H    0.623
A H    0.647
A H    0.631
A H    0.515
G C    0.631
R H    0.524
E H    0.657
S H    0.696
I H    0.757
K H    0.782
A H    0.809
Y H    0.807
L H    0.808
K H    0.824
K H    0.828
E H    0.829
I H    0.816
K H    0.795
K H    0.756
K H    0.513
G C    0.713
K C    0.634
R E    0.447
A E    0.636
V E    0.698
I E    0.668
A E    0.506
W C    0.598
END


