
PFRMAT SS
TARGET T0115
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0115
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-4266/target-align-4266.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 67.621
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0115
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.714/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 Jul 18 11:24:26 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-4266/target-align-4266.a2m
METHOD 
METHOD  guide seq name: T0115
METHOD ###end 0
MODEL 1
M C    0.728
R C    0.594
E C     0.52
I C     0.46
M C    0.416
K E    0.481
V E     0.53
R E    0.551
V E    0.556
K E    0.465
A C     0.54
P C    0.622
C C    0.464
T E    0.419
S E    0.509
A E     0.48
N E    0.414
L C    0.496
G C    0.642
V C    0.644
G C      0.6
F C    0.471
D C    0.411
V E    0.443
F E    0.482
G E    0.428
L E    0.458
C E    0.438
L E    0.441
K C    0.407
E C    0.518
P C    0.561
Y C     0.53
D E    0.409
V E    0.583
I E    0.616
E E    0.615
V E    0.594
E E    0.537
A E    0.459
I C    0.553
D C    0.656
D C    0.653
K C    0.533
E E     0.52
I E    0.616
I E    0.626
I E    0.595
E E    0.481
V C    0.463
D C    0.557
D C    0.592
K C    0.596
N C    0.622
I C    0.585
P C     0.56
T C    0.512
D C    0.509
P H    0.448
D H    0.544
K H    0.597
N H     0.64
V H    0.675
A H    0.699
G H    0.715
I H    0.722
V H    0.724
A H    0.736
K H    0.738
K H    0.733
M H    0.726
I H    0.722
D H    0.707
D H    0.665
F H    0.526
N C      0.6
I C    0.603
G C    0.623
K C    0.619
G C    0.586
V E    0.411
K E    0.576
I E    0.647
T E    0.651
I E    0.615
K E    0.471
K C    0.583
G C    0.634
V C    0.663
K C    0.686
A C    0.596
G C    0.601
S C    0.595
G C    0.623
L C    0.595
G C     0.63
S H    0.482
S H    0.585
A H    0.674
A H    0.701
S H    0.719
S H    0.736
A H    0.747
G H     0.75
T H    0.748
A H    0.754
Y H    0.753
A H    0.745
I H    0.746
N H    0.724
E H    0.704
L H    0.675
F H    0.558
K C    0.584
L C    0.627
N C    0.667
L C    0.631
D C    0.645
K H    0.686
L H    0.722
K H    0.728
L H    0.733
V H    0.728
D H    0.724
Y H    0.699
A H    0.669
S H    0.647
Y H    0.626
G H    0.567
E H    0.497
L H    0.483
A H    0.426
S E    0.342
S C    0.386
G C     0.47
A C    0.504
K C    0.536
H C    0.607
A C    0.672
D C    0.648
N C    0.624
V C    0.438
A H    0.363
P H    0.432
A H    0.399
I E      0.4
F C    0.341
G C    0.585
G C    0.577
F E    0.457
T E    0.557
M E    0.575
V E    0.524
T E    0.415
N C    0.524
Y C    0.594
E C    0.601
P C    0.575
L C    0.425
E E    0.448
V E    0.495
L E    0.467
H E    0.446
I C    0.409
P C    0.493
I C    0.572
D C    0.625
F C    0.619
K C    0.595
L C    0.437
D E    0.549
I E    0.664
L E    0.695
I E    0.699
A E    0.654
I E    0.494
P C    0.561
N C    0.617
I C    0.578
S C    0.571
I C    0.557
N C    0.618
T H    0.557
K H    0.671
E H    0.694
A H    0.692
R H    0.695
E H     0.68
I H    0.647
L H    0.558
P H    0.548
K H    0.525
A C     0.46
V C     0.54
G C    0.563
L H    0.531
K H     0.59
D H    0.632
L H     0.67
V H    0.678
N H    0.688
N H    0.679
V H    0.675
G H    0.692
K H    0.705
A H    0.726
C H    0.734
G H    0.734
M H    0.734
V H    0.741
Y H    0.746
A H    0.739
L H    0.721
Y H    0.685
N H    0.667
K C      0.5
D C    0.583
K H    0.686
S H    0.722
L H    0.732
F H     0.74
G H    0.743
R H    0.726
Y H    0.716
M H    0.704
M H    0.684
S H    0.694
D H    0.638
K H    0.631
V H    0.607
I H    0.557
E H    0.562
P H    0.566
V H    0.601
R H    0.577
G H    0.549
K H    0.535
L H    0.498
I C    0.477
P H    0.544
N H    0.598
Y H    0.717
F H    0.739
K H    0.753
I H    0.757
K H    0.768
E H    0.763
E H     0.76
V H    0.739
K H      0.7
D H    0.564
K C    0.604
V C    0.553
Y C    0.399
G E    0.456
I E    0.517
T E    0.525
I E     0.49
S C    0.483
G C     0.65
S C    0.701
G C     0.71
P C    0.611
S E    0.415
I E     0.55
I E    0.589
A E     0.58
F E    0.522
P C    0.481
K C    0.615
E H    0.506
E H    0.614
F H    0.658
I H    0.743
D H    0.771
E H    0.782
V H    0.779
E H    0.787
N H    0.792
I H    0.778
L H     0.77
R H    0.747
D H    0.714
Y H    0.539
Y C    0.564
E C    0.467
N E    0.461
T E    0.519
I E     0.53
R E    0.507
T E     0.46
E C    0.401
V C    0.478
G C    0.537
K C    0.526
G C    0.447
V E    0.409
E E    0.514
V E     0.52
V C    0.445
END


