
PFRMAT SS
TARGET T0121
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0121
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-6182/target-align-6182.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 1468.59
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0121
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.1435/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: Sun Aug 20 07:22:14 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-6182/target-align-6182.a2m
METHOD 
METHOD  guide seq name: T0121
METHOD ###end 0
MODEL 1
M C    0.643
A C    0.532
G E    0.466
V E    0.577
R E    0.575
L E    0.551
V E    0.478
D E    0.433
V E    0.495
W E    0.529
K E    0.552
V E    0.504
F C    0.404
G C    0.616
E C    0.605
V C    0.417
T E    0.508
A E    0.559
V E     0.53
R E     0.46
E E    0.442
L E    0.474
S E    0.531
L E    0.576
E E    0.583
V E    0.524
K C    0.524
D C    0.652
G C    0.656
E E     0.43
F E    0.643
M E    0.722
I E    0.737
L E    0.743
L E    0.684
G C    0.522
P C    0.697
S C    0.727
G C    0.661
C C     0.61
G C     0.53
K H    0.519
T H    0.574
T H     0.61
T H    0.639
L H    0.658
R H    0.665
M H    0.652
I H    0.644
A H    0.585
G C    0.452
L C     0.51
E C    0.554
E C    0.625
P C    0.637
S C    0.646
R C    0.621
G C    0.544
Q E    0.503
I E    0.635
Y E     0.64
I E    0.574
G C    0.536
D C    0.638
R C    0.558
L C    0.513
V C    0.454
A C    0.491
D C      0.5
P C    0.554
E C     0.61
K H    0.603
G H    0.637
I H    0.654
F H    0.679
V H     0.69
P H    0.686
P H    0.653
K H    0.549
D C    0.432
R C    0.479
D C    0.409
I E    0.508
A E    0.536
M E    0.542
V E    0.485
F C    0.422
Q C    0.512
S C    0.578
Y C    0.507
A C     0.48
L C    0.459
Y C    0.563
P C    0.576
H C    0.541
M C    0.481
T C    0.475
V H    0.615
Y H    0.643
D H     0.66
N H     0.64
I H    0.639
A H    0.628
F H    0.612
P H     0.56
L H    0.591
K H    0.602
L H    0.585
R H    0.509
K C    0.605
V C    0.632
P C    0.659
R H    0.548
Q H    0.634
E H    0.671
I H    0.686
D H    0.755
Q H    0.782
R H     0.78
V H    0.788
R H    0.798
E H    0.799
V H    0.792
A H    0.781
E H    0.759
L H    0.747
L H    0.652
G C    0.592
L C    0.599
T C    0.533
E H    0.442
L H    0.503
L H    0.472
N C    0.441
R C    0.459
K C     0.51
P C    0.482
R C    0.465
E C    0.449
L C    0.493
S C    0.606
G C    0.484
G H    0.521
Q H    0.638
R H    0.706
Q H    0.726
R H    0.728
V H    0.731
A H    0.735
L H    0.742
G H    0.746
R H    0.748
A H     0.73
I H    0.702
V H    0.629
R H    0.482
K C    0.698
P C    0.667
Q C    0.504
V E     0.58
F E     0.63
L E    0.617
M E    0.526
D C      0.5
E C    0.641
P C    0.634
L C    0.545
S C    0.538
N C    0.551
L C    0.598
D C    0.661
A H    0.681
K H    0.694
L H    0.707
R H    0.779
V H      0.8
R H    0.799
M H    0.811
R H     0.83
A H    0.837
E H    0.828
L H    0.823
K H    0.808
K H    0.792
L H    0.757
Q H    0.735
R H    0.696
Q H     0.64
L C    0.464
G C    0.662
V C    0.629
T E    0.565
T E    0.694
I E    0.724
Y E    0.709
V E     0.64
T E    0.463
H C    0.506
D C    0.562
Q H    0.608
V H    0.658
E H    0.675
A H    0.681
M H    0.677
T H    0.659
M H    0.636
G H    0.522
D C    0.463
R E    0.362
I E    0.555
A E    0.611
V E    0.614
M E     0.55
N C    0.418
R C    0.609
G C     0.65
V E    0.449
L E    0.589
Q E    0.583
Q E    0.521
V C    0.432
G C    0.636
S C    0.689
P H    0.606
D H    0.654
E H    0.668
V H    0.652
Y H    0.628
D H    0.572
K C    0.468
P C     0.54
A C    0.562
N C    0.555
T C    0.489
F C    0.417
V C    0.358
A C    0.348
G C     0.38
F C     0.42
I C    0.475
G C    0.544
S C    0.591
P C    0.647
P C     0.61
M C    0.474
N H    0.453
F H    0.515
L H    0.529
D H    0.554
A H    0.541
I H    0.508
V H    0.437
T C    0.528
E C    0.587
D C    0.595
G C    0.526
F C    0.476
V C    0.428
D C    0.441
F C    0.469
G C     0.47
E C    0.456
F H     0.47
R H    0.482
L H    0.478
K H    0.456
L C    0.471
L C     0.51
P C    0.519
D H    0.516
Q H    0.597
F H    0.637
E H    0.664
V H    0.677
L H    0.678
G H     0.65
E H    0.652
L H    0.646
G H    0.613
Y H    0.652
V H    0.644
G H    0.636
R H    0.654
E H    0.644
V H    0.641
I H    0.615
F H    0.559
G H    0.477
I C    0.503
R C    0.576
P C    0.477
E H    0.508
D H    0.515
L H    0.559
Y H    0.556
D H     0.59
A H    0.649
M H    0.674
F H    0.678
A H    0.667
R H    0.668
V H    0.645
R H    0.632
V H    0.583
P H    0.553
G H    0.555
E H    0.515
N C    0.478
L C    0.531
V C    0.625
R C    0.688
A C    0.759
V C     0.75
V C    0.746
E C     0.69
I C    0.632
V C    0.581
E C    0.582
N C    0.608
L C    0.661
G C    0.698
S C      0.7
E C      0.6
R C    0.523
I C    0.462
V C    0.462
H C    0.499
L C    0.476
R H    0.412
V H    0.448
G H    0.476
G H    0.516
V H    0.554
T H    0.523
F H    0.438
V H    0.433
G H    0.401
A H    0.368
F C    0.455
R C    0.598
S C    0.771
E C    0.704
S C    0.588
R C    0.377
V E    0.489
R E      0.5
E E    0.462
G E    0.425
V E    0.474
E E    0.504
V E    0.531
D E    0.526
V E    0.499
V E    0.399
F H    0.404
D H    0.365
M E    0.372
K E    0.475
K E    0.551
I E    0.569
H E    0.602
I E    0.576
F E    0.413
D C    0.555
K C    0.685
T C    0.723
T C    0.766
G C    0.731
K C    0.669
A C    0.608
I C    0.614
F C    0.797
END


