
PFRMAT SS
TARGET T0120
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0120
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-25498/target-align-25498.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 2.01178
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0120
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.2254/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 27 05:38:51 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-25498/target-align-25498.a2m
METHOD 
METHOD  guide seq name: T0120
METHOD ###end 0
MODEL 1
M C    0.711
E C    0.559
R C    0.481
K C     0.39
I E    0.362
S E    0.375
R E    0.474
I E    0.518
H E    0.565
L E    0.582
V E    0.492
S C    0.575
E C    0.671
P C    0.673
S C    0.585
I C    0.382
T E    0.383
H E    0.423
F E    0.494
L E    0.533
Q E    0.553
V E    0.567
S E    0.492
W H    0.503
E H    0.523
K H    0.523
T H     0.48
L H    0.478
E H    0.439
S C    0.494
G C    0.667
F E    0.529
V E    0.759
I E    0.784
T E    0.762
L E    0.682
T C    0.534
D C    0.696
G C    0.722
H C    0.632
S C    0.472
A C    0.418
W E    0.475
T E    0.459
G E    0.432
T E    0.513
V E    0.434
S C    0.591
E H     0.51
S H     0.51
E H    0.541
I H    0.505
S H    0.517
Q H     0.61
E H    0.588
A H    0.656
D H    0.653
D H    0.725
M H     0.73
A H    0.695
M H    0.669
E H    0.657
K H    0.613
G C    0.463
K C    0.502
Y H    0.452
V H     0.66
G H     0.72
E H    0.747
L H    0.758
R H    0.767
K H    0.771
A H    0.744
L H    0.724
L H    0.651
S H    0.507
G C    0.663
A C    0.712
G C    0.778
P C      0.7
A C     0.62
D C    0.514
V E    0.478
Y E    0.611
T E    0.654
F E    0.645
N E    0.536
F E    0.453
S C    0.527
K H    0.409
E H    0.434
S H    0.468
C H    0.442
Y H    0.449
F H    0.452
F H    0.462
F H     0.42
E H    0.445
K C    0.414
N C    0.509
L C    0.419
K C    0.409
D C    0.382
V H    0.342
S E    0.385
F E    0.455
R E    0.448
L E    0.374
G C    0.491
S C    0.487
F C    0.467
N C    0.518
L H    0.435
E H    0.423
K H    0.432
V C    0.466
E C    0.576
N C    0.731
P H    0.564
A H    0.673
E H    0.685
V H    0.682
I H    0.687
R H    0.701
E H    0.695
L H    0.659
I H    0.617
C H    0.603
Y H    0.588
C H    0.521
L H     0.53
D H    0.446
T H    0.452
I H     0.52
A H    0.547
E H    0.566
N H    0.518
Q H    0.547
A H    0.544
K H     0.57
N H    0.558
E H    0.609
H H    0.616
L H    0.643
Q H    0.653
K H    0.691
E H    0.678
N H    0.635
E H    0.728
R H    0.705
L H    0.682
L H    0.638
R H     0.55
D H    0.505
W H    0.736
N H    0.692
D H    0.706
V H    0.645
Q H    0.656
G H    0.629
R H    0.611
F H    0.715
E H     0.73
K H    0.718
C H    0.685
V H    0.629
S H    0.603
A H    0.785
K H    0.797
E H    0.811
A H    0.795
L H    0.778
E H    0.773
T H    0.753
D H    0.756
L H    0.757
Y H    0.745
K H    0.693
R H    0.595
F H    0.523
I H      0.5
L H    0.492
V H    0.483
L H    0.481
N H    0.472
E H    0.545
K H      0.6
K H    0.679
T H    0.668
K H    0.711
I H    0.743
R H     0.77
S H    0.776
L H    0.783
H H    0.781
N H    0.819
K H    0.811
L H      0.8
L H    0.794
N H    0.771
A H    0.792
A H    0.783
Q H    0.787
E H     0.78
R H     0.76
E H    0.775
K H    0.775
D H    0.759
I H    0.762
K H    0.751
Q H    0.727
E H    0.516
G C    0.668
E C    0.599
T C    0.411
A E    0.426
I E    0.485
C E    0.413
S C    0.377
E C     0.39
M C    0.425
T C    0.486
A C    0.567
D C    0.676
R C     0.69
D C    0.747
P C    0.696
V C    0.584
Y C    0.548
D C     0.64
E C    0.633
S C    0.679
T C    0.679
D C    0.688
E C    0.518
E C    0.549
S C    0.606
E C    0.616
N C    0.657
Q C    0.515
T C    0.527
D C    0.503
L H    0.484
S C    0.443
G C    0.426
L C    0.404
A H    0.409
S H    0.413
A H    0.395
A H    0.364
V C    0.357
S C    0.518
K C     0.59
D C    0.643
D C    0.589
S C    0.486
I E    0.371
I E    0.363
S C    0.427
S C    0.472
L C    0.537
D C    0.594
V C    0.424
T C    0.455
D C     0.47
I C    0.488
A C    0.599
P C    0.518
S C     0.47
R H    0.615
K H    0.636
R H    0.684
R H    0.717
Q H    0.734
R H    0.731
M H     0.71
Q H    0.682
R H    0.591
N H    0.497
L C    0.515
G C    0.728
T C    0.719
E C    0.669
P C    0.625
K C    0.545
M C    0.531
A C    0.611
P C    0.585
Q C    0.526
E H    0.484
N H    0.463
Q H    0.511
L H     0.53
Q H    0.513
E H    0.477
K C    0.487
E C    0.544
N C    0.652
S C    0.705
R C    0.757
P C    0.752
D C     0.73
S C    0.688
S C    0.683
L C    0.691
P C    0.705
E C      0.6
T C    0.601
S C    0.619
K C    0.471
K H    0.439
E H    0.441
H H     0.38
I C    0.345
S C    0.417
A H    0.478
E H    0.431
N C    0.465
M C    0.515
S C    0.532
L H    0.699
E H    0.697
T H    0.696
L H    0.621
R H    0.531
N C    0.517
S C    0.716
S C    0.788
P H    0.557
E H    0.619
D H    0.623
L H    0.592
F H    0.541
D H    0.514
E H    0.472
I C    0.638
END


