
PFRMAT SS
TARGET T0100
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0100
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-4215/target-align-4215.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 29.4636
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0100
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.alpha.3936/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: Tue Jun 13 21:50:44 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-4215/target-align-4215.a2m
METHOD 
METHOD  guide seq name: T0100
METHOD ###end 0
MODEL 1
A C    0.553
T C    0.524
T C    0.569
Y C    0.544
N C    0.427
A E    0.615
V E     0.69
V E    0.673
S E    0.514
K C    0.457
S C    0.585
S C    0.648
S C    0.669
D C    0.666
G C    0.688
K C    0.645
T C    0.589
F C    0.428
K C    0.399
T C    0.397
I H    0.684
A H    0.702
D H     0.72
A H    0.697
I H    0.677
A H    0.621
S H    0.557
A C     0.48
P C    0.577
A C    0.613
G C    0.654
S C    0.689
T C    0.637
P C    0.437
F E    0.659
V E    0.743
I E    0.762
L E    0.741
I E    0.685
K E      0.5
N C    0.551
G C    0.548
V E    0.497
Y E    0.547
N E    0.533
E E    0.528
R E    0.579
L E     0.65
T E    0.637
I E    0.546
T C     0.49
R C    0.604
N C    0.596
N C    0.471
L E    0.593
H E    0.667
L E    0.671
K E    0.596
G C     0.46
E C    0.599
S C    0.675
R C    0.681
N C    0.646
G C     0.53
A E    0.544
V E     0.66
I E    0.664
A E    0.573
A E    0.437
A C    0.521
T C    0.463
A C     0.45
A C    0.451
G C    0.491
T C    0.508
L C    0.453
K C    0.491
S C    0.524
D C    0.493
G C    0.528
S C    0.581
K C    0.582
W C    0.543
G C    0.534
T C    0.443
A E    0.415
G E    0.387
S E    0.413
S E    0.475
T E    0.536
I E    0.573
T E    0.567
I E     0.53
S E     0.44
A C    0.497
K C    0.587
D C    0.507
F E    0.414
S E    0.506
A E    0.515
Q E    0.495
S E      0.5
L E    0.542
T E    0.557
I E    0.562
R E     0.51
N C    0.403
D C    0.514
F C    0.622
D C    0.663
F C    0.672
P C    0.671
A C    0.674
N C    0.642
Q C    0.597
A C    0.517
K C    0.512
S C    0.563
D C    0.651
S C     0.61
D C    0.604
S C    0.578
S C    0.562
K C    0.576
I C    0.593
K C    0.574
D C    0.556
T C     0.51
Q C    0.358
A E    0.463
V E    0.539
A E    0.561
L E    0.581
Y E    0.563
V E    0.523
T E    0.459
K C     0.54
S C    0.588
G C     0.59
D C    0.584
R C    0.398
A E    0.461
Y E    0.577
F E    0.591
K E    0.549
D E    0.489
V E    0.459
S E    0.508
L E    0.541
V E    0.492
G E    0.418
Y C      0.4
Q C    0.442
D C    0.496
T E    0.481
L E    0.575
Y E    0.574
V E    0.501
S C    0.454
G C    0.549
G C    0.546
R C     0.41
S E    0.513
F E    0.595
F E    0.559
S E    0.419
D C    0.388
C E    0.463
R E    0.575
I E    0.594
S E    0.548
G E    0.472
T E    0.476
V E    0.481
D E    0.472
F E    0.643
I E    0.654
F E    0.609
G C    0.414
D C    0.549
G C    0.414
T E    0.478
A E    0.579
L E    0.598
F E    0.563
N E    0.465
N C    0.405
C E     0.42
D E    0.557
L E    0.603
V E    0.598
S E    0.544
R E    0.421
Y C    0.554
R C    0.647
A C    0.616
D C    0.602
V C    0.608
K C    0.594
S C    0.607
G C    0.659
N C    0.656
V C    0.534
S E    0.408
G E    0.438
Y E    0.599
L E    0.628
T E     0.56
A E    0.445
P C    0.583
S C    0.678
T C    0.677
N C    0.703
I C    0.675
N C    0.664
Q C    0.637
K C    0.614
Y C    0.478
G E    0.432
L E    0.599
V E    0.672
I E    0.671
T E    0.628
N E    0.519
S E    0.431
R E    0.538
V E    0.576
I E    0.507
R C    0.448
E C      0.6
S C    0.647
D C    0.623
S C    0.506
V C    0.468
P C    0.467
A C    0.455
K C    0.448
S C    0.372
Y E    0.431
G E    0.448
L E    0.378
G C    0.559
R C    0.607
P C    0.612
W C    0.467
H C     0.46
P C    0.476
T C    0.492
T C    0.555
T C    0.594
F C    0.577
S C    0.604
D C    0.643
G C    0.625
R C    0.522
Y C    0.508
A C     0.58
D C    0.629
P C    0.606
N C    0.601
A C    0.615
I C     0.64
G C    0.598
Q E    0.446
T E    0.664
V E    0.704
F E    0.674
L E    0.574
N C    0.408
T C    0.474
S C    0.428
M C    0.387
D C    0.408
N H    0.405
H H    0.384
I C    0.401
Y C    0.515
G C    0.583
W C    0.523
D C    0.497
K C    0.471
M C    0.473
S C    0.523
G C    0.565
K C    0.579
D C    0.582
K C    0.613
N C    0.704
G C    0.675
N C    0.549
T C     0.43
I E    0.402
W E     0.39
F C    0.422
N C    0.582
P C    0.552
E C    0.556
D C    0.412
S E    0.515
R E    0.568
F E    0.581
F E    0.555
E E    0.527
Y E    0.504
K C    0.521
S C    0.607
Y C    0.658
G C    0.778
A C    0.743
G C    0.727
A C    0.689
A C    0.644
V C     0.55
S C    0.545
K C    0.483
D C    0.445
R C    0.421
R C    0.468
Q C      0.5
L C     0.52
T C    0.526
D H     0.44
A H    0.491
Q H    0.487
A H    0.469
A H    0.439
E H    0.383
Y E    0.367
T E    0.425
Q E    0.395
S E    0.358
K E     0.39
V E    0.416
L C    0.421
G C    0.582
D C    0.603
W C    0.576
T C    0.493
P C    0.435
T C    0.458
L C    0.618
P C    0.744
END


