
PFRMAT SS
TARGET T0119
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0119
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-5990/target-align-5990.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 384.074
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0119
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.14782/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 27 05:57:02 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-5990/target-align-5990.a2m
METHOD 
METHOD  guide seq name: T0119
METHOD ###end 0
MODEL 1
M C    0.595
S C    0.591
N C    0.616
H C    0.611
Q C    0.461
V E     0.43
A E    0.502
L E    0.543
Q E    0.541
F E    0.496
E E    0.408
D C    0.478
G C    0.578
V C    0.577
T C    0.511
R E    0.388
F E    0.479
I E    0.509
C E     0.46
I C    0.435
A C    0.604
Q C    0.599
G C      0.5
E H    0.597
T H    0.629
L H    0.695
S H    0.724
D H     0.73
A H    0.732
A H    0.725
Y H    0.711
R H    0.686
Q H    0.548
Q C    0.687
I C    0.673
N C    0.617
I C    0.504
P C    0.507
M C    0.417
D C    0.406
C C     0.53
R C    0.578
E C     0.61
G C    0.638
E C    0.537
C C    0.531
G C    0.495
T C    0.416
C E    0.417
R E     0.49
A E    0.552
F E    0.573
C E    0.578
E E    0.474
S C    0.469
G C      0.6
N C     0.61
Y C    0.544
D C    0.583
M C     0.55
P C    0.562
E C    0.526
D C    0.499
N C     0.44
Y C     0.38
I C    0.403
E C    0.502
D C    0.497
A C    0.498
L C    0.534
T C    0.612
P H    0.608
E H    0.633
E H     0.64
A H    0.631
Q H    0.616
Q H    0.577
G C    0.552
Y C    0.513
V C    0.356
L E    0.415
A E    0.438
C E    0.412
Q E    0.395
C C     0.39
R C     0.48
P C    0.543
T C    0.583
S C    0.623
D C    0.599
A C    0.406
V E    0.493
F E    0.521
Q E    0.494
I E    0.453
Q C    0.397
A C    0.454
S C    0.485
S H    0.457
E H    0.478
V H    0.491
C H    0.429
K C    0.443
T C    0.558
K C    0.544
I C    0.478
H C    0.454
H C    0.408
F E    0.367
E E    0.414
G E    0.528
T E    0.583
L E    0.603
A E    0.574
R E     0.52
V E    0.488
E E    0.463
N E    0.416
L C     0.44
S C    0.561
D C    0.579
S C    0.505
T E    0.451
I E    0.542
T E    0.614
F E    0.637
D E    0.629
I E    0.596
Q E    0.426
L C    0.561
D C    0.669
D C    0.686
G C    0.683
Q C    0.665
P C    0.627
D C    0.586
I C    0.533
H C    0.544
F C    0.496
L C    0.588
A C    0.601
G C    0.602
Q C    0.477
Y E    0.633
V E    0.693
N E    0.701
V E    0.674
T E    0.614
L E     0.47
P C    0.561
G C    0.664
T C    0.587
T C    0.523
E C    0.462
T C    0.417
R E    0.428
S E    0.476
Y E    0.539
S E    0.525
F E    0.417
S C    0.501
S C    0.572
Q C    0.662
P C     0.68
G C    0.695
N C    0.678
R C    0.599
L E    0.441
T E    0.619
G E     0.66
F E    0.694
V E    0.704
V E    0.691
R E    0.659
N E    0.604
V E    0.441
P C    0.621
Q C    0.657
G C    0.645
K C    0.467
M H    0.431
S H    0.511
E H    0.601
Y H    0.606
L H    0.606
S H     0.59
V H     0.58
Q H    0.471
A C    0.522
K C    0.623
A C    0.592
G C    0.666
D C    0.632
K E    0.431
M E    0.564
S E    0.592
F E    0.587
T E    0.472
G C    0.562
P C    0.647
F C    0.616
G C    0.641
S C    0.545
F C    0.439
Y E    0.403
L C    0.437
R C    0.574
D C    0.646
V C    0.674
K C     0.67
R C     0.61
P C    0.439
V E    0.658
L E     0.71
M E    0.715
L E    0.681
A E    0.488
G C    0.616
G C    0.698
T C    0.622
G C    0.586
I H    0.417
A H    0.501
P H    0.593
F H    0.665
L H      0.7
S H    0.709
M H    0.724
L H    0.741
Q H    0.749
V H    0.739
L H    0.728
E H    0.693
Q H    0.604
K C    0.487
G C    0.656
S C    0.659
E C    0.644
H C    0.596
P C    0.425
V E    0.579
R E    0.643
L E    0.664
V E    0.656
F E    0.607
G E    0.508
V C     0.44
T C     0.57
Q C    0.638
D H    0.472
C H    0.546
D H    0.596
L H    0.609
V H     0.61
A H    0.617
L H    0.738
E H     0.78
Q H    0.786
L H    0.801
D H    0.797
A H    0.792
L H    0.769
Q H    0.746
Q H    0.717
K H    0.634
L C    0.601
P C    0.582
W C     0.51
F E    0.413
E E    0.545
Y E    0.595
R E    0.608
T E    0.614
V E    0.605
V E    0.561
A E    0.406
H C    0.554
A C    0.654
E C    0.659
S C    0.653
Q C     0.59
H C    0.564
E C    0.536
R C    0.519
K C    0.449
G C    0.394
Y H    0.343
V H    0.489
T H    0.584
G H    0.683
H H    0.699
I H    0.702
E H    0.704
Y H    0.687
D H    0.642
W H    0.563
L C    0.455
N C    0.574
G C    0.575
G C    0.631
E C    0.622
V C      0.5
D E    0.559
V E    0.672
Y E    0.707
L E    0.676
C E    0.503
G C    0.704
P C    0.715
V C    0.461
P H    0.547
M H    0.625
V H    0.703
E H    0.738
A H    0.748
V H     0.76
R H    0.774
S H     0.78
W H    0.776
L H    0.774
D H    0.761
T H    0.745
Q H    0.656
G C    0.602
I C    0.651
Q C    0.663
P C    0.451
A H    0.487
N H    0.444
F H    0.356
L E    0.438
F E    0.433
E E    0.344
K C    0.373
F C    0.488
S C    0.759
A C    0.874
N C    0.837
END


