
PFRMAT SS
TARGET T0087
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0087
METHOD  Using neural net overrep-2260-IDaa13-5-9-7-10-5-9-11-ehl-seeded2-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 EHL )
METHOD  The input amino acid frequencies were determined from
METHOD  alignment /projects/compbio/tmp/hmm-target99-alpha-8086/target-align-8086.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 27.037
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0087
METHOD  model_file: ./tmp.alpha.23167/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 May 12 04:14:25 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-8086/target-align-8086.a2m
METHOD 
METHOD  guide seq name: T0087
METHOD ###end 0
MODEL 1
M C    0.658
S C    0.633
K C    0.437
I E    0.669
L E     0.73
V E    0.739
F E    0.694
G E    0.561
H C    0.514
Q C    0.669
N C    0.805
P C    0.771
D C    0.787
S C    0.508
D C    0.489
A H    0.616
I H    0.678
G H    0.678
S H    0.709
S H    0.751
M H    0.754
A H    0.751
Y H    0.763
A H    0.766
Y H    0.771
L H    0.758
K H    0.751
R H    0.711
Q H    0.638
L C    0.484
G C    0.658
V C    0.672
D C    0.603
A C    0.449
Q E     0.54
A E    0.616
V E    0.611
A E    0.527
L C     0.47
G C    0.605
N C    0.688
P C    0.645
N C    0.654
E H    0.485
E H    0.512
T H    0.581
A H    0.611
F H    0.598
V H    0.603
L H    0.597
D H      0.6
Y H    0.589
F H    0.519
G H    0.448
I C    0.444
Q C    0.482
A C    0.535
P C    0.531
P C    0.481
V C    0.439
V C    0.437
K C    0.403
S C    0.436
A C    0.433
Q C    0.523
A C    0.461
E C    0.451
G C    0.474
A C     0.47
K C    0.422
Q E    0.519
V E    0.704
I E    0.752
L E    0.743
T E    0.655
D C    0.499
H C    0.679
N C    0.667
E C    0.631
F C    0.528
Q C    0.459
Q H    0.425
S C    0.418
I H    0.421
A C     0.46
D C    0.474
I C    0.451
R C    0.517
E C    0.513
V C    0.527
E C    0.496
V E    0.432
V E    0.562
E E     0.62
V E    0.637
V E    0.525
D C    0.475
H C    0.578
H C    0.583
R C    0.584
V C     0.58
A C     0.59
N C    0.587
F C    0.525
E C    0.486
T C    0.506
A C    0.541
N C    0.612
P C     0.57
L C    0.435
Y E    0.368
M E    0.463
R E    0.413
L C    0.465
E C    0.531
P C    0.542
V C    0.509
G C    0.555
S C    0.456
A H    0.639
S H    0.708
S H    0.722
I H    0.738
V H    0.755
Y H    0.765
R H    0.778
L H     0.77
Y H    0.764
K H    0.751
E H      0.7
N H    0.472
G C    0.631
V C    0.637
A C    0.615
I C    0.571
P C    0.601
K H    0.664
E H    0.691
I H      0.7
A H    0.709
G H    0.702
V H    0.697
M H    0.689
L H    0.659
S H    0.594
G H    0.543
L H    0.512
I H    0.477
S H    0.438
D C     0.49
T C    0.509
L C    0.499
L C    0.486
L C    0.481
K C    0.512
S C    0.562
P C    0.662
T C    0.651
T C    0.656
H C    0.677
A H    0.589
S H    0.611
D H    0.665
P H     0.77
A H    0.782
V H    0.789
A H    0.819
E H    0.826
D H    0.818
L H    0.806
A H    0.775
K H    0.751
I H    0.712
A H    0.495
G C    0.613
V C    0.622
D C    0.652
L H    0.699
Q H    0.735
E H    0.744
Y H    0.746
G H     0.75
L H    0.762
A H    0.762
M H    0.745
L H    0.709
K H    0.693
A H    0.581
G H    0.491
T C    0.502
N C    0.473
L C    0.465
A C     0.47
S C    0.476
K C    0.485
T C    0.486
A H    0.725
A H    0.761
Q H    0.765
L H    0.756
V H    0.741
D H    0.711
I H     0.64
D H    0.572
A H    0.559
K H    0.488
T H     0.41
F E    0.365
E E      0.4
L C    0.376
N C    0.505
G C    0.567
S C    0.524
Q C    0.445
V C    0.403
R C    0.431
V E    0.381
A E    0.432
Q E    0.506
V E    0.542
N E    0.556
T E    0.523
V E    0.429
D C    0.548
I H    0.512
N H    0.575
E H    0.624
V H    0.623
L H    0.611
E H    0.619
R H    0.686
Q H    0.705
N H    0.739
E H    0.737
I H    0.751
E H    0.782
E H     0.79
A H    0.782
I H    0.765
K H    0.761
A H    0.745
S H    0.727
Q H    0.705
A H    0.672
A H    0.548
N C    0.507
G C    0.548
Y C    0.479
S E    0.391
D E    0.541
F E    0.607
V E    0.633
L E     0.62
M E    0.569
I E    0.515
T E    0.392
D C    0.504
I C    0.407
L C    0.417
N C    0.464
S C    0.483
N H    0.448
S H    0.499
E H    0.534
I H    0.547
L H    0.541
A H    0.529
L H    0.504
G H    0.432
N C    0.435
N H    0.559
T H     0.62
D H    0.674
K H    0.669
V H    0.647
E H    0.664
A H     0.64
A H    0.579
F C    0.418
N C    0.566
F C     0.54
T C    0.475
L C    0.503
K C    0.579
N C    0.602
N C    0.578
H C    0.445
A C    0.358
F C    0.357
L H    0.385
A C    0.409
G C    0.418
A H      0.4
V H    0.398
S C    0.403
R C    0.479
K H     0.45
K H    0.505
Q H    0.471
V H    0.511
V H    0.583
P H    0.628
Q H    0.666
L H    0.667
T H    0.671
E H    0.664
S H    0.614
F H    0.441
N C    0.589
G C    0.663
END


