
PFRMAT SS
TARGET T0101
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0101
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-30813/target-align-30813.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 10.7526
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0101
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.29424/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: Fri Jun 16 18:09:20 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-30813/target-align-30813.a2m
METHOD 
METHOD  guide seq name: T0101
METHOD ###end 0
MODEL 1
A C    0.629
D C    0.662
C C    0.664
S C    0.674
S C    0.682
D C    0.669
L C    0.661
T C    0.662
S C    0.662
G C    0.661
I C    0.637
S C    0.563
T C    0.475
K C    0.418
R C    0.481
I E    0.441
Y E    0.566
Y E    0.603
V E     0.54
A C    0.571
P C    0.687
N C     0.69
G C    0.732
N C    0.719
S C    0.685
S C    0.717
N C     0.77
N C    0.739
G C    0.687
S C    0.648
S C    0.586
F C    0.591
N C    0.658
A C    0.645
P H    0.484
M H    0.569
S H    0.609
F H    0.714
S H    0.729
A H     0.74
A H    0.724
M H    0.706
A H     0.68
A H    0.645
V H    0.504
N C    0.604
P C    0.693
G C    0.701
E C    0.637
L E    0.558
I E    0.696
L E    0.696
L E     0.61
K C    0.538
P C    0.655
G C    0.597
T C    0.442
Y E    0.569
T E    0.591
I E    0.568
P E    0.463
Y C    0.501
T C    0.598
Q C    0.649
G C    0.709
K C    0.663
G C    0.632
N C    0.533
T E    0.484
I E    0.557
T E    0.549
F E    0.482
N C    0.447
K C    0.557
S C    0.605
G C    0.623
K C    0.637
D C    0.625
G C    0.647
A C    0.564
P E    0.435
I E    0.576
Y E    0.605
V E    0.624
A E    0.574
A E     0.48
A C    0.438
N C    0.572
C C    0.634
G C    0.637
R C    0.499
A E    0.445
V E    0.551
F E    0.541
D E    0.476
F E    0.428
S C    0.438
F C    0.541
P C    0.596
D C    0.568
S C    0.511
Q C    0.419
W H    0.417
V H    0.438
Q H    0.444
A H     0.43
S H    0.382
Y C    0.376
G C     0.53
F E    0.403
Y E    0.517
V E    0.528
T E    0.402
G C    0.403
D E    0.359
Y E    0.457
W E     0.48
Y E     0.44
F C    0.416
K C    0.536
G C    0.546
V C    0.371
E E    0.473
V E    0.489
T E     0.45
R E    0.386
A C    0.415
G C    0.536
Y C    0.504
Q C    0.508
G C    0.473
A E    0.557
Y E    0.639
V E    0.627
I E    0.504
G C     0.54
S C    0.662
H C     0.57
N C     0.54
T C    0.435
F C    0.377
E C    0.416
N C    0.411
T E    0.357
A E    0.429
F E    0.481
H E    0.462
H E    0.408
N C     0.47
R C    0.537
N C    0.597
T C     0.61
G C     0.58
L C    0.497
E C    0.431
I C    0.439
N C    0.553
N C    0.578
G C    0.515
G C    0.474
S C    0.437
Y H    0.423
N H     0.41
T H    0.417
V E    0.397
I E     0.41
N C    0.435
S C    0.443
D C    0.453
A C    0.469
Y C    0.456
R C    0.544
N C    0.669
Y C    0.642
D C    0.717
P C    0.715
K C    0.717
K C    0.698
N C    0.705
G C    0.656
S C    0.636
M C    0.607
A C     0.58
D C    0.587
G C    0.483
F C      0.4
G C    0.428
P C    0.427
K C      0.4
Q C    0.397
K C    0.436
Q C    0.512
G C    0.667
P C    0.661
G C    0.616
N C    0.436
R E    0.504
F E    0.552
V E    0.504
G E     0.49
C E    0.533
R E    0.543
A E    0.473
W C    0.377
E C    0.457
N C    0.506
S C    0.556
D C    0.626
D C    0.645
G C    0.675
F C    0.632
D C    0.655
L C    0.592
F C    0.586
D C    0.608
S C    0.604
P C    0.551
Q C    0.435
K E    0.463
V E    0.654
V E    0.659
I E    0.618
E E    0.487
N C     0.52
S C     0.51
W E    0.423
A E    0.433
F E    0.408
R C    0.456
N C    0.568
G C     0.61
I C    0.625
N C    0.626
Y C    0.599
W C    0.611
N C    0.634
D C    0.568
S C    0.445
A E    0.423
F E    0.462
A E    0.445
G C    0.455
N C    0.561
G C    0.604
N C    0.631
G C    0.511
F E    0.473
K E    0.524
L E    0.452
G C    0.573
G C    0.656
N C    0.635
Q C    0.542
A C    0.422
V E    0.337
G H    0.395
N H    0.469
H H    0.528
R H    0.534
I H    0.534
T H    0.545
R H    0.524
S H    0.484
V H    0.474
A H    0.441
F C    0.372
G C    0.508
N C     0.52
V C    0.482
S C    0.464
K C    0.534
G C     0.61
F C    0.551
D C    0.562
Q C    0.546
N C    0.553
N C    0.567
N C    0.616
A C    0.641
G C    0.646
G C    0.546
V E    0.507
T E    0.617
V E    0.634
I E    0.527
N C    0.457
N C    0.518
T E    0.456
S E    0.502
Y E    0.469
K C    0.506
N C    0.645
G C    0.646
I C    0.485
N E    0.458
Y E    0.464
G C     0.45
F C      0.5
G C    0.601
S C    0.516
N C    0.522
V C    0.457
Q C    0.481
S C    0.527
G C    0.637
Q C    0.597
K C    0.417
H C    0.406
Y C     0.36
F E    0.388
R C    0.472
N C    0.551
N C    0.547
V E    0.466
S E    0.552
L E    0.539
S C    0.419
A C    0.506
S C    0.541
V C     0.54
T C    0.592
V C    0.545
S C    0.512
N C    0.558
A C    0.549
D C    0.572
A C    0.529
K C    0.559
S C    0.549
N C    0.561
S C    0.467
W C    0.425
D C    0.482
T C    0.594
G C    0.654
P C    0.608
A C    0.473
A C    0.417
S C    0.463
A C    0.483
S C    0.539
D C    0.526
F E    0.372
V E    0.456
S E    0.426
L C    0.407
D C    0.548
T C    0.556
S C    0.515
L C    0.499
A C    0.498
T C    0.438
V C    0.397
S C    0.411
R C    0.408
D C    0.538
N C    0.643
D C    0.721
G C      0.7
T C     0.62
L C    0.481
P C    0.421
E C    0.411
T C    0.433
S E    0.428
L E    0.528
F E    0.564
R E    0.575
L E    0.548
S C    0.417
A C    0.571
N C    0.576
S C    0.415
K E    0.379
L E    0.394
I C    0.424
N C    0.546
A C    0.588
G C    0.643
T C    0.675
K C    0.667
E C    0.594
S C    0.546
N C    0.532
I C    0.487
S C    0.521
Y C     0.56
S C    0.624
G C    0.633
S C    0.596
A C    0.573
P C    0.565
D C    0.496
L C     0.44
G C    0.399
A E    0.429
F E    0.406
E C    0.431
R C    0.526
N C    0.651
END


