
PFRMAT SS
TARGET T0103
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0103
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-25342/target-align-25342.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 65.9281
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0103
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.17186/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 27 13:43:34 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-25342/target-align-25342.a2m
METHOD 
METHOD  guide seq name: T0103
METHOD ###end 0
MODEL 1
A C    0.695
A C    0.551
G C    0.524
T C    0.477
A C    0.445
K C    0.421
G C    0.473
H C    0.543
N C    0.657
P C    0.452
T H    0.469
E H     0.49
F H    0.461
P H    0.472
T H    0.446
I H    0.423
Y C    0.393
D C    0.424
A C    0.389
S C    0.399
S C    0.423
A C    0.463
P C    0.504
T C    0.583
A C     0.67
A C    0.682
N C    0.623
T E    0.474
T E    0.637
V E    0.706
G E    0.705
I E    0.707
I E    0.638
T C    0.443
I C    0.619
G C    0.654
G C      0.6
V C     0.61
S C    0.594
Q C    0.634
T C    0.651
L H    0.453
Q H    0.471
D H    0.511
L H     0.49
Q H    0.485
Q H    0.436
F H    0.427
T H    0.408
S H    0.415
A H    0.417
N C     0.48
G C    0.581
L C    0.576
A C    0.556
S C    0.503
V C    0.552
N C    0.627
T C    0.627
Q C    0.552
T C     0.47
I C     0.45
Q C    0.465
T C    0.532
G C     0.63
S C    0.687
S C    0.661
N C    0.564
G C    0.543
D C    0.581
Y C    0.601
S C    0.631
D C     0.62
D C    0.683
Q C    0.661
Q C    0.667
G C    0.663
Q C    0.636
G C    0.561
E C    0.428
W E    0.447
D E    0.486
L E     0.43
D E    0.367
S E    0.369
Q C    0.366
S C    0.524
I C    0.446
V E    0.396
G E     0.41
S C    0.459
A C    0.551
G C    0.575
G C    0.567
A C    0.387
V E    0.545
Q E    0.607
Q E    0.608
L E     0.52
L C    0.499
F C    0.606
Y C    0.658
M C    0.676
A C    0.661
D C    0.609
Q C    0.525
S H      0.4
A H    0.474
S H    0.512
G H    0.543
N H    0.578
T H    0.592
G H    0.602
L H     0.63
T H    0.639
Q H    0.644
A H    0.628
F H    0.603
N H    0.524
Q C    0.425
A C     0.45
V C    0.473
S C    0.542
D C    0.604
N C    0.648
V C    0.607
A C    0.512
K E    0.441
V E    0.632
I E    0.644
N E    0.602
V E     0.57
S E    0.423
L C    0.504
G C    0.645
W C    0.638
C C    0.634
E C    0.582
A C    0.592
D C    0.582
A C    0.548
N C    0.551
A C    0.574
D C    0.655
G C    0.539
T H     0.46
L H    0.566
Q H     0.63
A H     0.66
E H    0.694
D H    0.714
R H    0.746
I H    0.748
F H    0.757
A H    0.753
T H    0.753
A H    0.736
A H     0.71
A H    0.685
Q H    0.526
G C    0.641
Q C    0.484
T E    0.644
F E    0.718
S E    0.716
V E    0.657
S E    0.547
S C    0.447
G C    0.698
D C    0.767
E C    0.715
G C     0.72
V C    0.682
Y C     0.61
E C    0.574
C C    0.563
N C    0.615
N C    0.621
R C     0.67
G C    0.644
Y C    0.609
P C    0.577
D C    0.585
G C    0.566
S C    0.589
T C    0.565
Y C    0.583
S C    0.569
V C    0.582
S C    0.633
W C    0.695
P C    0.738
A C    0.642
S C    0.636
S C    0.671
P C    0.632
N C    0.488
V E    0.541
I E     0.63
A E    0.637
V E    0.612
G E    0.509
G E    0.474
T E     0.46
T C    0.418
L C    0.446
Y C    0.556
T C    0.581
T C    0.588
S C    0.499
A C    0.429
G C    0.448
A C    0.448
Y C    0.459
S C    0.575
N C    0.621
E C    0.631
T C    0.606
V C    0.527
W E    0.458
N E    0.536
E E    0.539
G E    0.573
L E    0.493
D C    0.543
S C    0.658
N C    0.665
G C     0.55
K E    0.437
L E    0.589
W E    0.576
A E    0.506
T C    0.436
G C     0.55
G C    0.656
G C    0.629
Y C    0.519
S C     0.47
V C    0.455
Y C    0.511
E C    0.576
S C    0.582
K C    0.574
P C    0.545
S C    0.495
W C    0.452
Q C    0.452
S C    0.478
V C      0.5
V C    0.562
S C    0.641
G C    0.613
T C    0.634
P C     0.57
G C    0.463
R C    0.413
R C    0.426
L C    0.496
L C    0.621
P C    0.597
D C    0.576
I C    0.456
S C     0.44
F C    0.435
D C    0.461
A C    0.509
A C    0.543
Q C    0.543
G C     0.49
T C    0.434
G E    0.428
A E    0.501
L E    0.534
I E    0.542
Y E    0.469
N C    0.495
Y C     0.62
G C    0.633
Q C    0.554
L C    0.451
Q E    0.424
Q E    0.452
I C    0.474
G C    0.635
G C    0.671
T C     0.59
S C    0.519
L C    0.456
A C    0.501
S C    0.503
P H    0.489
I H    0.563
F H    0.623
V H    0.645
G H    0.653
L H     0.66
W H    0.685
A H    0.692
R H    0.686
L H    0.679
Q H    0.666
S H    0.634
A H    0.562
N C    0.681
S C    0.676
N C    0.652
S C    0.568
L C    0.536
G C    0.564
F C    0.585
P C    0.636
A H    0.614
A H    0.684
S H    0.697
F H    0.702
Y H    0.706
S H    0.696
A H     0.69
I H    0.681
S H    0.648
S H     0.58
T C    0.519
P C    0.519
S C    0.526
L C    0.473
V C    0.454
H C     0.47
D C    0.513
V C     0.45
K C    0.476
S C    0.593
G C    0.687
N C    0.695
N C     0.62
G C    0.457
Y E    0.407
G E    0.395
G C    0.398
Y C    0.481
G C     0.56
Y C    0.535
N C     0.51
A C    0.513
G C    0.519
T C    0.508
G C     0.52
W C    0.515
D C    0.542
Y C    0.492
P C    0.465
T C     0.51
G C    0.612
W C    0.594
G C    0.562
S C    0.459
L C    0.423
D C    0.571
I H    0.611
A H    0.634
K H    0.653
L H    0.661
S H    0.734
A H    0.741
Y H    0.759
I H     0.76
R H    0.734
S H    0.664
N H    0.586
G C    0.499
F C    0.773
G C    0.773
H C    0.826
END


