
PFRMAT SS
TARGET T0127
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0127
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-3995/target-align-3995.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 174.165
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0127
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.20890/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 Aug 29 23:29:46 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-3995/target-align-3995.a2m
METHOD 
METHOD  guide seq name: T0127
METHOD ###end 0
MODEL 1
M C    0.638
T C    0.508
T H    0.512
A H    0.617
V H    0.618
A H     0.62
R H    0.577
L H    0.535
Q C    0.498
P C    0.601
S C    0.648
A C     0.59
S C    0.528
G H    0.465
A H    0.509
K H    0.499
T H    0.435
R C    0.452
P C    0.547
V C    0.437
F C    0.421
P H    0.425
F H    0.425
S H    0.454
A H    0.419
I H    0.401
V C    0.439
G C    0.575
Q H    0.633
E H    0.689
D H    0.715
M H    0.742
K H     0.76
L H     0.76
A H    0.753
L H    0.751
L H    0.742
L H    0.729
T H    0.702
A H     0.67
V H     0.59
D C    0.573
P C    0.662
G C    0.623
I C    0.598
G C    0.552
G E    0.433
V E    0.697
L E    0.729
V E    0.697
F E    0.556
G C    0.551
D C    0.686
R C     0.72
G C    0.669
T C    0.628
G C    0.479
K H    0.572
S H    0.633
T H    0.686
A H    0.708
V H    0.735
R H    0.736
A H    0.733
L H     0.73
A H    0.714
A H    0.676
L H    0.608
L C    0.492
P C    0.599
E C    0.542
I C    0.504
E C    0.462
A C    0.403
V C    0.374
E C    0.429
G C    0.537
C C    0.585
P C     0.59
V C    0.564
S C    0.548
S C    0.527
P C     0.52
N C    0.466
V C    0.438
E C    0.402
M H    0.365
I H    0.361
P H    0.355
D C     0.36
W C    0.396
A C    0.423
T C    0.453
V C    0.479
L C    0.525
S C    0.574
T C    0.543
N C    0.493
V C    0.373
I E    0.408
R E    0.427
K E    0.387
P C    0.409
T C    0.438
P C    0.431
V C    0.376
V C    0.422
D C    0.492
L C    0.562
P C    0.603
L C    0.557
G C    0.509
V C    0.475
S C    0.477
E H    0.629
D H    0.627
R H      0.6
V H    0.508
V H    0.442
G C    0.449
A C    0.433
L C      0.4
D C    0.437
I H    0.601
E H    0.587
R H    0.574
A H    0.461
I H     0.43
S C    0.433
K C    0.529
G C    0.575
E C    0.503
K C    0.436
A C    0.398
F C     0.45
E C    0.509
P C    0.513
G C    0.462
L H    0.428
L H    0.492
A H    0.539
R H    0.547
A H    0.488
N C    0.455
R C    0.629
G C    0.578
Y E    0.551
L E    0.604
Y E    0.579
I E    0.451
D H    0.373
E C    0.474
C C    0.483
N C    0.466
L C    0.489
L C    0.543
E C    0.538
D H     0.75
H H    0.754
I H    0.763
V H    0.791
D H    0.793
L H    0.794
L H    0.791
L H     0.79
D H    0.773
V H     0.76
A H    0.737
Q H    0.698
S H    0.568
G C    0.598
E C     0.49
N E    0.458
V E    0.516
V E    0.499
E E    0.421
R C    0.378
D C    0.541
G C    0.613
L C    0.462
S E    0.429
I E    0.429
R C    0.402
H C    0.495
P C    0.544
A C    0.535
R C    0.468
F E     0.59
V E    0.651
L E    0.661
V E    0.627
G E    0.556
S E    0.482
G C     0.47
N C     0.64
P C    0.611
E C    0.578
E C    0.556
G C    0.608
D C    0.592
L C    0.614
R C    0.584
P H    0.647
Q H    0.672
L H    0.684
L H    0.653
D H    0.616
R H    0.568
F C     0.46
G C    0.488
L C     0.39
S E    0.454
V E    0.513
E E    0.497
V E    0.418
L C    0.511
S C    0.615
P C    0.649
R C    0.651
D H    0.486
V H    0.684
E H    0.703
T H    0.714
R H    0.734
V H    0.744
E H    0.737
V H    0.748
I H    0.746
R H    0.735
R H    0.732
R H     0.72
D H    0.701
T H    0.674
Y H    0.563
D H    0.495
A C    0.465
D C    0.531
P H      0.5
K H    0.552
A H    0.576
F H    0.558
L H    0.558
E H    0.551
E H    0.562
W H    0.551
R H    0.567
P H    0.582
K H    0.592
D H    0.674
M H    0.709
D H    0.721
I H    0.742
R H    0.778
N H    0.778
Q H    0.768
I H    0.773
L H    0.766
E H     0.76
A H    0.751
R H    0.733
E H    0.697
R H    0.649
L H    0.523
P C    0.451
K C    0.536
V C    0.541
E C    0.555
A C    0.588
P C    0.566
N H    0.727
T H    0.742
A H    0.753
L H    0.775
Y H    0.781
D H    0.779
C H    0.778
A H    0.779
A H    0.768
L H    0.746
C H    0.733
I H    0.746
A H    0.714
L H    0.627
G C    0.505
S C    0.601
D C    0.617
G C    0.581
L H    0.707
R H    0.741
G H    0.754
E H    0.776
L H    0.783
T H    0.785
L H    0.795
L H    0.808
R H     0.81
S H    0.807
A H    0.801
R H    0.798
A H    0.791
L H    0.791
A H     0.77
A H     0.75
L H    0.721
E H    0.597
G C    0.606
A C    0.604
T C    0.536
A C    0.397
V C    0.388
G C    0.503
R H    0.685
D H    0.699
H H    0.709
L H    0.755
K H    0.769
R H    0.765
V H    0.754
A H    0.741
T H    0.721
M H    0.711
A H    0.704
L H    0.696
S H    0.683
H H    0.657
R H    0.631
L H    0.583
R H    0.515
R C    0.427
D C    0.527
P C    0.546
L C    0.554
D C    0.548
E C    0.562
A C    0.578
G C    0.613
S C    0.527
T H    0.454
A H     0.53
R H     0.58
V H    0.652
A H    0.687
R H    0.683
T H    0.674
V H    0.678
E H    0.651
E H    0.575
T H    0.485
L C    0.502
P C    0.744
END


