
PFRMAT SS
TARGET T0111
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0111
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-26890/target-align-26890.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 13.8854
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0111
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.13499/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: Thu Jul 13 14:31:49 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-26890/target-align-26890.a2m
METHOD 
METHOD  guide seq name: T0111
METHOD ###end 0
MODEL 1
S C    0.632
K C    0.459
I E    0.356
V H    0.392
K E    0.412
I E    0.489
I E    0.484
G E    0.445
R E    0.433
E E    0.464
I E    0.438
I H    0.419
D C    0.428
S C    0.531
R C    0.679
G C    0.779
N C    0.801
P C    0.617
T E    0.581
V E    0.644
E E    0.655
A E    0.635
E E    0.608
V E    0.606
H E    0.558
L E    0.453
E C    0.518
G C    0.597
G C     0.57
F C    0.428
V E    0.468
G E    0.486
M E      0.5
A E    0.488
A E    0.492
A C    0.524
P C    0.669
S C    0.704
G C    0.748
A C    0.732
S C    0.686
T C    0.578
G C     0.56
S H    0.457
R H     0.52
E H    0.541
A H    0.524
L H    0.497
E H    0.465
L H    0.384
R C    0.499
D C    0.635
G C    0.672
D C    0.674
K C    0.592
S C    0.524
R C    0.418
F C    0.397
L C    0.492
G C    0.537
K C    0.434
G H    0.463
V H    0.549
T H    0.602
K H    0.629
A H     0.64
V H    0.651
A H    0.638
A H    0.604
V H    0.621
N H    0.617
G H    0.639
P H    0.604
I H    0.582
A H    0.518
Q H    0.629
A H    0.614
L H    0.608
I H    0.491
G C    0.619
K C     0.62
D C    0.621
A H    0.448
K H    0.477
D H    0.483
Q H    0.644
A H    0.639
G H    0.637
I H    0.647
D H     0.64
K H    0.675
I H    0.644
M H    0.621
I H    0.571
D H    0.519
L C    0.463
D C    0.678
G C    0.716
T C    0.695
E C    0.646
N C    0.619
K H    0.449
S H    0.442
K H    0.466
F H    0.421
G C    0.552
A H    0.545
N H    0.609
A H    0.672
I H    0.671
L H    0.669
A H    0.668
V H    0.677
S H    0.685
L H    0.746
A H    0.754
N H     0.76
A H    0.767
K H     0.78
A H    0.765
A H    0.747
A H    0.735
A H    0.708
A H    0.686
K H    0.583
G C     0.62
M C    0.633
P C    0.523
L H    0.614
Y H    0.653
E H    0.646
H H    0.637
I H    0.636
A H    0.677
E H    0.663
L H    0.626
N H    0.494
G C    0.629
T C    0.692
P C    0.653
G C      0.6
K C    0.525
Y C     0.43
S E    0.455
M C    0.504
P C      0.6
V C    0.547
P C    0.531
M E    0.483
M E    0.558
N E    0.561
I E    0.601
I E    0.517
N C    0.543
G C     0.64
G C    0.628
E C    0.597
H C    0.577
A C    0.603
D C    0.656
N C    0.649
N C    0.563
V C    0.476
D C     0.45
I H    0.367
Q E    0.376
E E    0.472
F E    0.558
M E    0.593
I E    0.563
Q C    0.432
P C    0.578
V C    0.616
G C    0.663
A C     0.56
K C     0.53
T C    0.477
V H    0.702
K H    0.721
E H    0.754
A H    0.752
I H    0.766
R H    0.758
M H    0.723
G H    0.719
S H    0.752
E H    0.758
V H    0.757
F H    0.771
H H    0.772
H H     0.77
L H    0.769
A H    0.761
K H    0.754
V H    0.738
L H    0.725
K H    0.702
A H    0.676
K H     0.57
G C    0.478
M C    0.626
N C    0.542
T C    0.498
A C    0.551
V C    0.581
G C    0.673
D C    0.706
E C    0.679
G C    0.693
G C    0.674
Y C    0.623
A C    0.683
P C    0.679
N C    0.637
L C    0.545
G C    0.551
S C    0.548
N H    0.487
A H    0.737
E H    0.762
A H    0.763
L H    0.804
A H    0.809
V H    0.812
I H     0.81
A H    0.814
E H    0.816
A H    0.805
V H    0.789
K H    0.772
A H    0.752
A H    0.593
G C    0.675
Y C    0.634
E C    0.598
L C    0.616
G C    0.635
K C    0.514
D E    0.491
I E    0.614
T E    0.639
L E     0.63
A E    0.577
M E    0.541
D E    0.442
C H    0.335
A H    0.405
A H    0.482
S H    0.471
E H    0.437
F H    0.406
Y C    0.381
K C    0.508
D C    0.584
G C    0.614
K C    0.511
Y E    0.423
V E     0.47
L E    0.459
A C    0.396
G C    0.432
E C    0.509
G C    0.615
N C    0.641
K C    0.525
A C    0.477
F C    0.521
T C    0.664
S H    0.692
E H    0.766
E H     0.78
F H     0.78
T H    0.799
H H    0.802
F H    0.802
L H    0.795
E H    0.788
E H    0.776
L H    0.751
T H    0.713
K H     0.66
Q H    0.598
Y C    0.601
P C    0.635
I E    0.514
V E    0.569
S E    0.536
I E     0.44
E C    0.566
D C    0.685
G C    0.663
L C    0.645
D C    0.689
E H    0.591
S H    0.596
D H     0.59
W H    0.712
D H    0.708
G H    0.707
F H    0.713
A H     0.71
Y H    0.697
Q H    0.661
T H    0.617
K H    0.611
V H    0.547
L C    0.441
G C    0.617
D C    0.594
K C    0.466
I E    0.552
Q E    0.643
L E    0.653
V E    0.572
G C    0.508
D C    0.639
D C    0.546
L E    0.401
F E     0.45
V E    0.424
T C    0.537
N C    0.678
T H    0.595
K H    0.644
I H    0.652
L H    0.662
K H    0.675
E H    0.658
G H    0.604
I H    0.546
E H    0.489
K H    0.558
G H    0.472
I C    0.439
A C    0.473
N C    0.426
S E     0.47
I E     0.56
L E    0.588
I E    0.572
K E    0.454
F C    0.364
N C    0.417
Q H    0.435
I H    0.468
G H    0.428
S H    0.466
L H    0.597
T H    0.623
E H    0.673
T H    0.685
L H    0.713
A H    0.711
A H    0.716
I H    0.711
K H     0.71
M H    0.699
A H     0.69
K H    0.666
D H    0.621
A H    0.467
G C    0.648
Y C    0.541
T E    0.475
A E    0.606
V E     0.66
I E    0.625
S E    0.544
H C    0.457
R C    0.618
S C    0.671
G C    0.704
E C    0.687
T C    0.657
E C    0.473
D H    0.476
A H    0.547
T H    0.556
I H    0.586
A H    0.616
D H    0.616
L H    0.605
A H    0.589
V H    0.549
G H    0.486
T H    0.401
A C    0.463
A C    0.497
G C    0.483
Q H    0.386
I H    0.393
K H    0.393
T C    0.478
G C    0.679
S C     0.62
M C    0.555
S C    0.582
R C    0.505
S H    0.476
D H    0.609
R H    0.624
V H    0.719
A H    0.742
K H    0.753
Y H    0.801
N H    0.803
Q H    0.819
L H     0.82
I H    0.808
R H    0.789
I H    0.775
E H    0.787
E H    0.813
A H    0.795
L H    0.729
G C    0.547
E C    0.532
K C    0.473
A C    0.408
P E    0.376
Y E    0.444
N C    0.396
G C    0.503
R C    0.508
K C      0.5
E C    0.621
I C    0.669
K C    0.744
G C    0.796
Q C    0.784
A C    0.833
END


