
PFRMAT SS
TARGET T0116
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0116
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-30545/target-align-30545.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 101.719
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0116
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.26425/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 25 06:16:51 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-30545/target-align-30545.a2m
METHOD 
METHOD  guide seq name: T0116
METHOD ###end 0
MODEL 1
M C    0.642
E C    0.563
G C    0.565
M C    0.577
L C    0.635
K C    0.692
G C    0.534
E C    0.509
G C    0.525
P C     0.46
G C    0.476
P C    0.484
L C    0.556
P C    0.623
P H    0.581
L H    0.616
L H    0.683
Q H    0.699
Q H    0.688
Y H    0.678
V H    0.655
E H    0.635
L H    0.601
R H    0.578
D H    0.517
Q C    0.473
Y C    0.631
P C    0.603
D C    0.538
Y E    0.558
L E    0.625
L E    0.637
L E    0.629
F E    0.594
Q E    0.505
V C    0.468
G C    0.592
D C    0.484
F E    0.391
Y E     0.46
E E    0.453
C H    0.387
F H    0.402
G H    0.463
E H    0.553
D H    0.636
A H    0.688
E H    0.689
R H    0.684
L H    0.679
A H     0.68
R H    0.683
A H    0.671
L H    0.627
G H    0.541
L H      0.5
V H    0.449
L E    0.374
T E    0.402
H E      0.4
K C    0.413
T C     0.53
S C    0.621
K C    0.662
D C    0.623
F C    0.606
T C    0.576
T C    0.464
P C    0.435
M E    0.402
A C    0.414
G C    0.486
I C    0.584
P C     0.65
L H    0.552
R H    0.588
A H    0.602
F H    0.658
E H    0.682
A H    0.704
Y H    0.703
A H     0.73
E H    0.746
R H     0.74
L H    0.729
L H    0.707
K H    0.683
M H    0.588
G C    0.644
F C    0.601
R E     0.51
L E    0.632
A E    0.625
V E    0.617
A E    0.554
D E    0.438
Q C    0.444
V C    0.511
E C    0.582
P C    0.655
A H    0.522
E H    0.552
E H    0.591
A H    0.515
E C    0.459
G C     0.59
L C    0.501
V C    0.399
R H    0.422
R H    0.421
E H    0.382
V E     0.46
T E    0.452
Q E    0.444
L E    0.428
L C    0.427
T C    0.673
P C    0.694
G C    0.682
T C      0.6
L C    0.513
L C    0.522
Q C    0.539
E C    0.465
S C    0.452
L C    0.444
L C    0.486
P C    0.581
R C    0.567
E C    0.587
A C    0.574
N C    0.569
Y E    0.374
L E    0.526
A E    0.577
A E    0.592
I E    0.582
A E    0.527
T C    0.482
G C    0.613
D C    0.565
G E    0.462
W E    0.555
G E    0.578
L E     0.61
A E    0.621
F E    0.623
L E    0.586
D E     0.48
V C    0.477
S C    0.556
T C    0.568
G C    0.528
E E     0.46
F E    0.555
K E    0.573
G E    0.547
T E    0.427
V C     0.43
L C    0.507
K C    0.598
S C    0.645
K H     0.51
S H     0.63
A H    0.671
L H    0.693
Y H    0.701
D H    0.708
E H    0.701
L H    0.689
F H    0.648
R H    0.582
H C    0.479
R C    0.683
P C    0.562
A C    0.421
E E    0.448
V E     0.57
L E    0.569
L E    0.448
A C    0.558
P C    0.598
E C    0.581
L C    0.547
L C    0.535
E C    0.459
N C    0.453
G H    0.492
A H    0.538
F H    0.563
L H    0.581
D H     0.57
E H     0.58
F H    0.578
R H    0.561
K H    0.546
R H    0.476
F H    0.458
P H    0.423
V C    0.402
M C    0.424
L C    0.444
S C    0.488
E C    0.425
A C    0.417
P H     0.42
F C    0.433
E H    0.449
P H    0.467
E H    0.476
G H    0.448
E H    0.443
G C    0.476
P H    0.442
L H    0.583
A H    0.655
L H    0.669
R H    0.685
R H    0.698
A H    0.707
R H    0.714
G H    0.699
A H    0.698
L H      0.7
L H    0.706
A H    0.699
Y H    0.689
A H     0.68
Q H    0.662
R H    0.648
T H    0.544
Q H    0.448
G H    0.473
G C    0.443
A C    0.441
L C    0.465
S C      0.5
L C    0.452
Q C    0.458
P C    0.458
F C    0.436
R C    0.366
F E     0.38
Y E    0.374
D C    0.411
P C    0.438
G C    0.493
A C    0.446
F E    0.356
M E     0.45
R E    0.482
L E    0.431
P C    0.511
E H    0.628
A H    0.653
T H    0.664
L H     0.68
R H    0.667
A H    0.658
L H    0.639
E H    0.571
V H    0.539
F H    0.395
E C    0.446
P C    0.532
L C    0.564
R C    0.636
G C    0.669
Q C    0.646
D C    0.496
T C    0.383
L H    0.609
F H    0.616
S H    0.629
V H    0.604
L H    0.583
D H    0.464
E H    0.466
T C    0.419
R C    0.417
T C    0.467
A H    0.524
P H    0.564
G H    0.595
R H    0.642
R H    0.657
L H    0.663
L H    0.665
Q H    0.649
S H    0.629
W H     0.57
L H    0.507
R C    0.421
H C    0.669
P C    0.665
L C    0.601
L C    0.614
D C     0.65
R H    0.667
G H    0.684
P H    0.707
L H    0.739
E H    0.742
A H     0.75
R H    0.756
L H    0.771
D H    0.763
R H    0.774
V H    0.793
E H    0.799
G H    0.788
F H    0.771
V H    0.747
R H    0.699
E H    0.664
G H    0.687
A H    0.698
L H    0.711
R H    0.732
E H     0.74
G H    0.737
V H    0.741
R H    0.741
R H    0.737
L H    0.709
L H    0.689
Y H    0.608
R H    0.562
L C    0.466
A C    0.497
D H    0.469
L H    0.774
E H    0.777
R H     0.79
L H    0.775
A H    0.768
T H    0.753
R H    0.747
L H     0.72
E H    0.666
L H      0.6
G C    0.491
R C    0.516
A C    0.546
S C    0.588
P H    0.661
K H    0.695
D H    0.701
L H    0.729
G H    0.724
A H    0.721
L H    0.727
R H     0.73
R H     0.72
S H    0.708
L H    0.715
Q H    0.697
I H    0.687
L H    0.702
P H    0.723
E H     0.73
L H     0.74
R H    0.751
A H    0.747
L H    0.737
L H    0.716
G H    0.647
E H    0.568
E H    0.468
V C    0.443
G C    0.473
L C    0.502
P C    0.503
D C    0.491
L H    0.634
S H    0.661
P H    0.695
L H    0.735
K H    0.754
E H    0.756
E H    0.748
L H    0.739
E H    0.717
A H      0.7
A H    0.666
L H     0.62
V H    0.576
E H    0.511
D C     0.44
P H    0.517
P H    0.537
L H     0.52
K H    0.462
V H    0.402
S C    0.532
E C    0.553
G C    0.517
G C    0.419
L E    0.435
I E     0.42
R C    0.452
E C    0.547
G C    0.605
Y C     0.59
D C    0.594
P H    0.643
D H    0.655
L H    0.762
D H    0.776
A H    0.791
L H     0.79
R H      0.8
A H    0.798
A H    0.793
H H    0.798
R H    0.802
E H    0.799
G H    0.791
V H    0.807
A H     0.82
Y H    0.815
F H    0.815
L H    0.819
E H    0.822
L H    0.816
E H    0.811
E H    0.811
R H      0.8
E H    0.768
R H    0.743
E H    0.712
R H    0.669
T H    0.517
G C    0.623
I C    0.626
P C    0.579
T C    0.451
L E    0.423
K E      0.5
V E     0.54
G E    0.525
Y E    0.497
N E    0.425
A C    0.442
V C    0.477
F C    0.453
G C    0.448
Y E    0.552
Y E    0.614
L E    0.619
E E    0.595
V E    0.531
T C    0.461
R C    0.492
P C    0.469
Y H    0.473
Y H    0.452
E H    0.418
R C    0.435
V C     0.56
P C    0.586
K C    0.522
E C    0.409
Y E     0.47
R E    0.505
P E    0.492
V E    0.459
Q E    0.387
T C    0.407
L C     0.45
K C    0.537
D C    0.532
R C    0.393
Q E    0.432
R E    0.499
Y E    0.464
T C    0.485
L C    0.511
P H    0.663
E H    0.689
M H     0.73
K H    0.742
E H    0.745
K H    0.745
E H    0.746
R H    0.768
E H    0.772
V H    0.775
Y H    0.762
R H    0.765
L H    0.769
E H     0.77
A H    0.774
L H    0.772
I H    0.772
R H    0.766
R H    0.773
R H    0.765
E H    0.771
E H    0.793
E H    0.799
V H    0.792
F H    0.796
L H    0.806
E H    0.798
V H    0.792
R H    0.784
E H    0.784
R H    0.773
A H    0.758
K H    0.743
R H    0.733
Q H    0.722
A H    0.718
E H     0.73
A H    0.739
L H    0.749
R H    0.744
E H    0.745
A H    0.738
A H    0.742
R H    0.739
I H    0.731
L H    0.725
A H    0.705
E H    0.699
L H    0.693
D H    0.672
V H     0.71
Y H    0.713
A H    0.712
A H    0.703
L H    0.714
A H    0.701
E H    0.685
V H    0.678
A H    0.659
V H    0.627
R H    0.593
Y C    0.471
G C    0.656
Y C    0.595
V C     0.53
R C    0.559
P C    0.513
R C    0.455
F C    0.438
G C    0.601
D C    0.584
R C     0.38
L E    0.524
Q E    0.549
I E    0.518
R E     0.38
A C    0.511
G C    0.642
R C    0.679
H C     0.69
P C    0.532
V E    0.394
V E     0.42
E E    0.388
R C    0.404
R C    0.538
T C    0.597
E C    0.588
F C    0.477
V C     0.52
P C    0.619
N C    0.619
D C    0.523
L E    0.444
E E    0.489
M E    0.432
A C    0.558
H C    0.637
E C     0.45
L E    0.654
V E    0.739
L E    0.777
I E    0.742
T E    0.597
G C    0.639
P C    0.741
N C    0.734
M C    0.671
A C    0.712
G C     0.66
K H    0.449
S H    0.576
T H    0.628
F H    0.643
L H    0.676
R H    0.698
Q H    0.712
T H    0.711
A H    0.698
L H    0.693
I H    0.694
A H     0.69
L H    0.689
L H    0.691
A H    0.681
Q H    0.654
V H    0.579
G C    0.516
S C     0.56
F C    0.527
V C    0.574
P C    0.624
A C    0.469
E C    0.439
E H    0.428
A C    0.454
H C    0.433
L C    0.378
P C    0.487
L H    0.516
F H    0.571
D H    0.577
G H    0.503
I E    0.427
Y E    0.454
T E    0.383
R E    0.385
I C    0.408
G C    0.615
A C    0.528
S C    0.498
D H     0.51
D H    0.512
L H    0.547
A H    0.521
G H    0.489
G C    0.489
K C     0.44
S H    0.505
T H    0.614
F H    0.633
M H    0.647
V H    0.687
E H    0.703
M H    0.724
E H    0.736
E H    0.743
V H    0.739
A H    0.736
L H    0.728
I H    0.716
L H    0.702
K H     0.64
E H    0.571
A C    0.522
T C    0.597
E C    0.528
N C    0.544
S C    0.393
L E    0.471
V E    0.598
L E    0.593
L E    0.489
D H    0.368
E H    0.427
V C    0.424
G C    0.578
R C    0.641
G C    0.649
T C    0.635
S C    0.635
S H    0.476
L H    0.544
D H    0.581
G H    0.631
V H     0.67
A H    0.693
I H    0.706
A H    0.711
T H    0.726
A H    0.731
V H    0.733
A H    0.746
E H    0.748
A H    0.733
L H    0.699
H H    0.683
E H    0.657
R H    0.554
R C    0.549
A C    0.521
Y C    0.347
T E    0.545
L E    0.579
F E    0.563
A E    0.465
T H    0.356
H C    0.394
Y H    0.575
F H    0.617
E H     0.62
L H    0.621
T H     0.61
A H     0.61
L H    0.568
G C    0.425
L C    0.514
P C    0.518
R C    0.493
L C    0.388
K E    0.404
N E     0.48
L E    0.511
H E    0.519
V E    0.534
A E    0.529
A E    0.541
R E    0.528
E E    0.467
E C     0.47
A C    0.604
G C    0.619
G C    0.496
L E     0.49
V E    0.565
F E    0.586
Y E    0.586
H E     0.58
Q E    0.575
V E    0.548
L E    0.419
P C    0.476
G C    0.608
P C    0.598
A C    0.609
S C    0.552
K C    0.458
S H    0.529
Y H    0.573
G H    0.569
V H    0.569
E H    0.583
V H    0.657
A H    0.682
A H    0.686
M H    0.675
A H    0.605
G C    0.629
L C    0.706
P C    0.685
K H    0.685
E H    0.704
V H    0.711
V H    0.738
A H    0.754
R H    0.767
A H     0.78
R H    0.778
A H    0.774
L H    0.757
L H    0.742
Q H    0.727
A H    0.732
M H    0.705
A H    0.708
A H    0.708
R H    0.694
R H    0.688
E H    0.697
G H    0.704
A H    0.683
L H    0.703
D H    0.708
A H    0.715
V H     0.73
L H    0.752
E H    0.771
R H    0.765
L H     0.76
L H    0.749
A H    0.729
L H    0.666
D H    0.573
P H    0.545
D H    0.478
R H    0.478
L C    0.455
T C    0.499
P H    0.701
L H    0.753
E H    0.766
A H    0.778
L H    0.786
R H    0.783
L H    0.773
L H    0.771
Q H    0.775
E H    0.753
L H    0.721
K H     0.65
A H    0.546
L C    0.628
A H    0.934
L H    0.916
G H    0.884
A H    0.596
P H    0.506
L H    0.732
D H    0.683
T H    0.566
M C    0.549
K C    0.760
G C    0.979
END

