
PFRMAT SS
TARGET T0106
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0106
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-5901/target-align-5901.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 26.7106
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0106
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.8122/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  6 00:44:36 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-5901/target-align-5901.a2m
METHOD 
METHOD  guide seq name: T0106
METHOD ###end 0
MODEL 1
A C    0.641
A C    0.576
C C    0.533
E C    0.452
P E    0.398
V E    0.464
R E    0.439
I E    0.398
P C    0.389
L E    0.365
C C    0.391
K C    0.472
S C    0.515
L C    0.544
P C    0.601
W C    0.512
E C    0.525
M C    0.455
T C     0.44
K C    0.468
M C    0.625
P C    0.632
N C    0.599
H C     0.55
L C    0.583
H C    0.629
H C    0.487
S C     0.48
T C    0.484
Q H    0.665
A H     0.69
N H      0.7
A H    0.702
I H     0.69
L H    0.693
A H    0.676
M H    0.681
E H    0.665
Q H    0.653
F H    0.623
E H    0.586
G H    0.581
L H    0.554
L H    0.514
G H    0.456
T C     0.44
H C    0.508
C C    0.482
S H    0.449
P H    0.576
D H    0.591
L H     0.61
L H    0.607
F H    0.608
F H    0.594
L H    0.574
C H    0.532
A H    0.531
M H     0.45
Y C     0.41
A C    0.646
P C    0.637
I C    0.555
C C    0.556
T C    0.588
I C    0.604
D C    0.636
F C    0.607
Q C    0.628
H C    0.666
E C     0.66
P C    0.599
I C    0.592
K C    0.631
P C    0.474
C H    0.463
K H    0.538
S H    0.569
V H    0.611
C H     0.59
E H    0.629
R H    0.631
A H    0.614
R H    0.627
Q H    0.607
G H    0.582
C H    0.544
E H    0.537
P H    0.571
I H    0.588
L H    0.609
I H    0.592
K H    0.588
Y H    0.517
R C    0.646
H C    0.638
S C    0.614
W C    0.671
P C    0.583
E C    0.487
S C    0.413
L C    0.431
A C    0.462
C C    0.446
D C    0.512
E C     0.52
L C    0.674
P C    0.697
V C    0.678
Y C    0.713
D C    0.728
R C    0.704
G C    0.644
V C    0.455
C C    0.418
I C    0.458
S C    0.585
P C    0.632
E C    0.606
A C    0.653
I C    0.583
V C     0.53
T C    0.601
A C    0.711
D C     0.79
G C    0.845
A C    0.861
D C    0.842
END


