
PFRMAT SS
TARGET T0089
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0089
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-18073/target-align-18073.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 61.9588
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0089
METHOD  model_file: ./tmp.alpha.11463/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 19 17:34:52 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-18073/target-align-18073.a2m
METHOD 
METHOD  guide seq name: T0089
METHOD ###end 0
MODEL 1
M C     0.67
I C    0.549
D C    0.512
L C    0.454
S C    0.494
K C    0.511
T C    0.529
V C    0.423
F E    0.572
Y E    0.655
T E    0.674
S E    0.658
I E    0.605
D E    0.474
I C    0.568
G C    0.696
S C    0.591
R C    0.501
Y E    0.461
I E    0.613
K E    0.676
G E    0.716
L E    0.702
V E    0.673
L E    0.591
G E    0.504
K E     0.44
R C    0.442
D C    0.614
Q C    0.665
E E    0.457
W E    0.599
E E    0.653
A E     0.69
L E    0.658
A E    0.558
F E    0.434
S C      0.5
S C    0.448
V C     0.42
K C    0.411
S C    0.426
R C    0.435
G C    0.432
L C    0.438
D C    0.504
E C    0.525
G C    0.541
E C    0.419
I E    0.456
K C    0.399
D C    0.555
A H    0.713
I H    0.735
A H    0.739
F H    0.724
K H    0.765
E H    0.764
S H     0.76
V H    0.777
N H    0.772
T H    0.784
L H     0.77
L H    0.786
K H     0.79
E H    0.792
L H    0.789
E H     0.76
E H    0.745
Q H      0.7
L H    0.621
Q C    0.599
K C    0.617
S C    0.493
L C    0.472
R C    0.567
S C    0.572
D C    0.392
F E    0.556
V E    0.596
I E    0.597
S E    0.512
F E    0.403
S C    0.507
S C    0.488
V C    0.472
S E    0.429
F E    0.488
E E    0.515
R E    0.492
E E    0.399
D C    0.493
T C    0.452
V E    0.486
I E    0.547
E E    0.588
R E    0.613
D E    0.572
F E    0.477
G C    0.546
E C    0.655
E C    0.637
K C    0.595
R C    0.522
S C    0.411
I C    0.424
T C    0.654
L H    0.725
D H    0.787
I H    0.786
L H    0.803
S H     0.81
E H     0.82
M H    0.812
Q H     0.81
S H    0.814
E H    0.811
A H    0.782
L H    0.754
E H    0.697
K H    0.639
L H    0.516
K C    0.471
E C    0.484
N C    0.512
G C    0.538
K C     0.47
T E    0.437
P E    0.546
L E    0.547
H E    0.481
I E    0.426
F C    0.486
S C    0.527
K C    0.424
R E    0.416
Y E    0.515
L E    0.515
L E    0.394
D C    0.584
D C    0.609
E C    0.556
R C    0.501
I C    0.534
V C    0.537
F C    0.552
N C    0.706
P C    0.552
L C    0.481
D C    0.501
M C    0.491
K C     0.45
A C    0.462
S C    0.448
K C     0.38
I E    0.408
A E    0.481
I E    0.515
E E    0.531
Y E    0.605
T E    0.641
S E    0.669
I E    0.655
V E    0.559
V C    0.439
P C    0.544
L H    0.456
K H    0.537
V H    0.619
Y H    0.675
E H    0.735
M H    0.742
F H    0.771
Y H    0.773
N H    0.767
F H    0.766
L H    0.757
Q H    0.762
D H    0.752
T H    0.631
V C    0.607
K C    0.656
S C    0.479
P E    0.456
F E    0.494
Q E    0.557
L E    0.597
K E    0.572
S E    0.427
S C     0.45
L H    0.479
V H    0.614
S H    0.666
T H    0.669
A H    0.664
E H    0.652
G H    0.617
V H    0.511
L C    0.498
T C    0.588
T C    0.592
P C    0.506
E C    0.482
K C    0.504
D C     0.57
R C    0.558
G C    0.573
V E    0.581
V E    0.706
V E    0.732
V E    0.695
N E    0.556
L C    0.543
G C    0.754
Y C    0.774
N C    0.739
F C    0.544
T E    0.466
G E    0.585
L E    0.685
I E    0.693
A E    0.692
Y E    0.632
K E    0.457
N C     0.58
G C    0.609
V E    0.489
P E     0.61
I E    0.628
K E     0.55
I C    0.452
S C    0.532
Y C    0.427
V E    0.414
P C    0.457
V C      0.5
G C    0.639
M H     0.48
K H     0.52
H H    0.553
V H    0.574
I H    0.611
K H    0.725
D H    0.726
V H    0.751
S H     0.76
A H    0.755
V H    0.738
L H    0.701
D H    0.602
T H    0.472
S C     0.46
F H    0.638
E H    0.626
E H    0.682
S H    0.761
E H    0.762
R H     0.75
L H    0.711
I H    0.696
I H    0.656
T H    0.628
H H    0.572
G H    0.481
N H    0.445
A C    0.432
V C    0.452
Y C    0.503
N C    0.538
D C     0.54
L C    0.558
K C    0.567
E C    0.535
E C    0.386
E E     0.47
I E    0.498
Q E    0.453
Y E    0.388
R C    0.408
G C    0.402
L C    0.441
D C    0.536
G C    0.586
N C    0.608
T C    0.589
I C    0.562
K C    0.453
T C    0.392
T C    0.442
T C     0.61
A H    0.809
K H    0.856
K H    0.859
L H    0.861
S H    0.872
V H    0.883
I H    0.868
I H    0.854
H H    0.867
A H    0.861
R H    0.855
L H    0.857
R H     0.88
E H    0.864
I H    0.853
M H    0.851
S H    0.854
K H     0.86
S H    0.869
K H    0.881
K H    0.875
F H    0.863
F H    0.856
R H    0.821
E H    0.807
V H    0.671
E C    0.586
A C    0.634
K C    0.628
I C    0.511
V C    0.457
E H    0.439
E H    0.439
G C    0.429
E H     0.45
I C     0.42
G C    0.426
I C    0.538
P C    0.579
G C    0.567
G E     0.48
V E    0.725
V E    0.789
L E    0.761
T E    0.572
G C    0.636
G C    0.652
G C    0.512
A C    0.442
K C    0.441
I C    0.441
P H    0.546
R H    0.618
I H    0.744
N H    0.778
E H    0.794
L H    0.784
A H    0.783
T H    0.774
E H    0.752
V H    0.719
F H     0.59
K C    0.569
S C    0.611
P C    0.514
V E    0.447
R E    0.526
T E    0.513
G C    0.431
C C    0.531
Y C    0.594
A C    0.585
N C    0.622
S C    0.691
D C    0.646
R C    0.627
P C    0.579
S C    0.524
I C    0.457
I C    0.472
N C    0.605
A C     0.57
D C    0.435
E H     0.43
V H    0.423
A C    0.393
N C     0.58
D C    0.773
P H    0.474
S H    0.575
F H    0.597
A H    0.588
A H    0.583
A H    0.599
F H    0.595
G H     0.57
N H    0.552
V H    0.566
F H    0.559
A H    0.542
V H    0.474
S H    0.402
E C    0.379
N C    0.468
P C    0.559
Y C    0.559
E C    0.545
E C    0.496
T C    0.503
P C    0.529
V C    0.566
K C     0.61
S C    0.615
E C    0.548
N C    0.496
P H    0.492
L H    0.598
K H     0.62
K H    0.629
I H    0.647
F H    0.629
R H    0.648
L H    0.594
F H    0.533
K H    0.549
E H    0.482
L C    0.453
M C    0.526
E C    0.603
END


