
PFRMAT SS
TARGET T0117
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0117
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-20228/target-align-20228.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 53.3544
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0117
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.24422/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: Wed Jul 26 18:07:34 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-20228/target-align-20228.a2m
METHOD 
METHOD  guide seq name: T0117
METHOD ###end 0
MODEL 1
M C    0.632
A C     0.54
E C    0.488
A C    0.506
A C    0.449
S C    0.403
C C    0.397
A C    0.446
R C    0.539
K C    0.639
G C    0.699
T C    0.697
K C    0.651
Y C    0.624
A C    0.599
E C    0.572
G C    0.561
T C    0.578
Q C     0.57
P C    0.483
F E    0.481
T E    0.693
V E    0.748
L E    0.732
I E    0.687
E E    0.521
G C    0.602
N C     0.58
I C    0.495
G C      0.5
S C    0.511
G C    0.545
K H    0.506
T H    0.567
T H    0.624
Y H    0.674
L H    0.714
N H    0.728
H H    0.732
F H    0.733
E H    0.726
K H    0.698
Y H    0.644
K H    0.478
N C    0.627
D C    0.614
I C    0.468
C E    0.475
L E     0.54
L E    0.474
T C    0.466
E C    0.546
P C    0.542
V C    0.397
E H    0.414
K H    0.423
W H    0.416
R H    0.389
N C    0.367
V C    0.441
N C    0.574
G C    0.579
V C    0.493
N H    0.451
L H    0.543
L H    0.599
E H    0.614
L H    0.609
M H    0.571
Y H    0.515
K H    0.465
D C    0.562
P H    0.532
K H     0.55
K H    0.586
W H    0.549
A H    0.573
M H    0.591
P H    0.607
F H     0.63
Q H    0.627
S H    0.622
Y H    0.619
V H    0.595
T H    0.572
L H    0.526
T H     0.57
M H    0.618
L H    0.633
Q H    0.623
S H    0.599
H H    0.575
T H    0.494
A C    0.453
P C    0.506
T C    0.584
N C    0.625
K C     0.64
K C    0.593
L E     0.44
K E    0.594
I E    0.625
M E    0.559
E E    0.426
R C    0.416
S C    0.486
I C    0.425
F C    0.409
S H    0.454
A H    0.516
R H    0.543
Y H    0.576
C H    0.586
F H      0.6
V H    0.632
E H    0.651
N H    0.646
M H    0.627
R H    0.604
R H    0.589
N H     0.52
G C     0.61
S C    0.604
L C    0.578
E C    0.624
Q H    0.615
G H    0.638
M H    0.648
Y H    0.685
N H    0.688
T H     0.69
L H    0.705
E H    0.698
E H    0.707
W H    0.703
Y H    0.686
K H    0.669
F H    0.628
I H    0.558
E H    0.532
E H    0.472
S C    0.468
I C    0.479
H C    0.564
V C    0.628
Q C    0.681
A C    0.652
D C    0.604
L E     0.56
I E    0.677
I E    0.723
Y E    0.705
L E    0.657
R E    0.517
T C    0.557
S C    0.713
P H    0.621
E H    0.708
V H     0.74
A H    0.744
Y H     0.77
E H    0.769
R H    0.765
I H    0.749
R H    0.735
Q H    0.719
R H    0.618
A C    0.615
R C    0.647
S C    0.616
E C    0.489
E C    0.466
S C    0.458
C C    0.484
V C    0.509
P C    0.576
L H     0.73
K H    0.754
Y H    0.762
L H    0.785
Q H    0.801
E H    0.795
L H    0.781
H H    0.765
E H    0.763
L H    0.752
H H     0.75
E H    0.754
D H    0.761
W H    0.748
L H    0.736
I H    0.703
H H    0.669
Q H    0.568
R H    0.486
R H    0.429
P C    0.555
Q C    0.559
S C    0.561
C C    0.483
K E    0.403
V E    0.581
L E    0.618
V E    0.624
L E    0.573
D E    0.431
A C    0.512
D C    0.597
L C    0.558
N C    0.549
L H    0.402
E H    0.394
N H    0.458
I H    0.471
G H    0.456
T H    0.471
E H    0.517
Y H    0.554
Q H    0.708
R H    0.722
S H    0.717
E H    0.737
S H    0.759
S H    0.765
I H     0.76
F H    0.764
D H    0.759
A H     0.76
I H     0.74
S H    0.688
S H    0.622
N C    0.494
Q C    0.483
Q C    0.425
P C    0.362
S C    0.358
P C    0.373
V C    0.362
L C    0.392
V C    0.447
S C    0.573
P C    0.578
S C     0.57
K H    0.521
R H    0.566
Q H    0.564
R H    0.524
V H    0.474
A H    0.394
R C    0.529
END


