
PFRMAT SS
TARGET T0114
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0114
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-beta-4290/target-align-4290.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 1.86607
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0114
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.5809/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: Thu Jul 13 15:08:57 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-beta-4290/target-align-4290.a2m
METHOD 
METHOD  guide seq name: T0114
METHOD ###end 0
MODEL 1
M C    0.645
I C    0.562
N C    0.659
R C    0.581
T C    0.576
D C    0.611
C C    0.642
N C    0.676
E C    0.572
N C    0.563
S C    0.447
Y E    0.412
L E    0.477
E E    0.499
I E    0.482
H E    0.373
N C    0.514
N C     0.59
E C    0.668
G C    0.731
R C    0.653
D C    0.609
T E    0.403
L E    0.538
C E     0.53
F E    0.496
A C    0.402
N C    0.529
A C    0.618
G C    0.672
T C    0.544
M C    0.507
P C    0.439
V E    0.599
A E    0.615
I E    0.661
Y E    0.619
G E    0.481
V E    0.483
N E    0.473
W E    0.598
V E    0.573
E E    0.475
S C    0.583
G C    0.713
N C    0.713
N C     0.57
V E    0.542
V E    0.696
T E    0.686
L E    0.674
Q E     0.63
F E    0.601
Q E    0.483
R C    0.397
N C    0.497
L C    0.501
S C    0.652
D C    0.746
P C    0.663
R C     0.53
L C     0.37
E C    0.358
T E    0.437
I E    0.505
T E    0.481
L E    0.412
Q H     0.35
K C    0.375
W C    0.425
G C    0.611
S C    0.636
W C    0.628
N C    0.747
P C    0.707
G C    0.642
H C    0.497
I E    0.367
H E    0.411
E E    0.488
I E    0.538
L E    0.537
S E    0.565
I E    0.581
R E    0.585
I E    0.518
Y C    0.603
END


