
PFRMAT SS
TARGET T0094
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0094
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-alpha-27917/target-align-27917.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 2.60547
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0094
METHOD  model_file: ./tmp.alpha.14561/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 May 25 12:21:21 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-alpha-27917/target-align-27917.a2m
METHOD 
METHOD  guide seq name: T0094
METHOD ###end 0
MODEL 1
M C    0.684
E H    0.599
E H    0.663
V H    0.669
K H     0.65
K H    0.603
D H    0.521
V H    0.485
Y H    0.433
S E    0.429
V E    0.468
W E    0.449
A E    0.371
L C    0.634
P C    0.761
D C    0.512
E H    0.545
E H    0.568
S H    0.593
E H    0.746
P H    0.827
R H    0.844
F H    0.885
K H    0.897
K H    0.895
L H    0.889
M H    0.882
E H     0.88
A H    0.851
L H    0.784
R H    0.749
S H    0.705
E H    0.637
F H    0.481
T C    0.608
G C    0.766
P C     0.72
R C     0.61
F C     0.58
V C    0.651
P C    0.647
H C    0.504
V E    0.519
T E    0.599
V E    0.584
A E    0.442
V C    0.422
S C    0.461
A C    0.421
Y C      0.4
L C    0.474
T C    0.601
A H    0.727
D H    0.779
E H    0.807
A H    0.816
K H    0.823
K H    0.816
M H    0.793
F H    0.779
E H    0.765
S H    0.711
A H    0.609
C H    0.492
D C    0.518
G C    0.574
L C    0.499
K C    0.407
A E    0.462
Y E    0.461
T E    0.429
A E    0.446
T E    0.457
V E    0.397
D C    0.396
R E    0.387
V E    0.403
S C     0.47
T C    0.528
G C    0.572
T C    0.474
F E    0.441
F E    0.543
F E    0.629
Q E    0.621
C E    0.638
V E    0.676
F E    0.685
L E    0.675
L E    0.638
L E    0.524
Q C    0.431
T C    0.529
T C    0.502
P H    0.452
E H    0.519
V H    0.565
M H     0.57
E H    0.563
A H    0.557
G H    0.525
E H    0.492
H H    0.471
C H    0.451
K H    0.445
N H    0.441
H C    0.379
F C    0.416
N C    0.517
C C    0.548
S C    0.574
T C    0.603
T C    0.609
T C    0.547
P C    0.494
Y C    0.447
M C    0.491
P C    0.486
H H    0.444
L H    0.512
S H    0.534
L H    0.541
L H    0.524
Y H    0.562
A H    0.515
E H    0.439
L C    0.447
T C    0.539
E H    0.689
E H    0.694
E H    0.675
K H    0.654
K H    0.658
N H    0.613
A H    0.624
Q H    0.627
E H     0.63
K H    0.597
A H    0.534
Y H    0.435
T H    0.358
L C    0.385
D C    0.529
S C    0.542
S C    0.567
L C    0.564
D C    0.623
G C     0.56
L C     0.48
S C    0.382
F E    0.419
R E    0.448
L E    0.443
N E    0.384
R E    0.429
L E    0.472
A E    0.499
L E    0.536
C E    0.497
K E    0.416
T C    0.552
D C    0.661
T C    0.643
E C    0.594
D C     0.57
K C    0.582
T C    0.542
L C    0.488
E C    0.475
T C    0.414
W H    0.353
E E    0.415
T E    0.452
V E    0.424
A E    0.382
V C    0.354
C C    0.368
N C    0.415
L C    0.492
N C    0.638
P C    0.755
END


