
PFRMAT SS
TARGET T0088
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0088
METHOD  Using neural net overrep-2260-IDaa13-5-9-7-10-5-9-11-ehl-seeded2-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 EHL )
METHOD  The input amino acid frequencies were determined from
METHOD  alignment /projects/compbio/tmp/hmm-target99-alpha-4709/target-align-4709.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 2.00263
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0088
METHOD  model_file: ./tmp.alpha.3069/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: Fri May 12 06:32:33 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-4709/target-align-4709.a2m
METHOD 
METHOD  guide seq name: T0088
METHOD ###end 0
MODEL 1
A C    0.448
V E    0.441
S E    0.498
F E    0.536
I E    0.493
G C    0.514
S C    0.625
T C    0.672
E C    0.596
N C    0.618
D C    0.632
V C    0.653
G C    0.756
P C    0.727
S C    0.726
Q C    0.678
G C    0.679
S C    0.627
Y C    0.527
S C    0.532
S C     0.47
T C    0.445
H C    0.399
A C    0.417
M C    0.484
D C    0.602
N C    0.661
L C    0.665
P C    0.562
F E    0.508
V E    0.558
Y E    0.485
N C    0.523
T C    0.646
G C    0.654
Y C    0.603
N C    0.523
I C     0.44
G C    0.466
Y C    0.445
Q C    0.485
N C     0.52
A C    0.541
N C    0.478
V E    0.476
W E    0.564
R E     0.59
I E    0.552
S C    0.425
G C    0.554
G C    0.522
F E    0.507
C E     0.61
V E    0.625
G C    0.467
L C    0.583
D C    0.648
G C    0.661
K C    0.606
V C    0.455
D C    0.479
L C    0.446
P E    0.463
V E    0.604
V E    0.653
G E    0.575
S C    0.497
L C    0.611
D C    0.715
G C    0.667
Q C     0.61
S E     0.41
I E    0.462
Y E     0.41
G C    0.458
L C    0.451
T C    0.415
E H    0.517
E H    0.541
V H    0.518
G H    0.408
L E    0.412
L E     0.49
I E    0.482
W E    0.493
M E    0.399
G C    0.606
D C    0.677
T C    0.639
N C    0.615
Y C    0.543
S C    0.542
R C    0.527
G C    0.557
T C    0.485
A C    0.443
M C    0.497
S C    0.613
G C    0.666
N C    0.669
S C    0.585
W H    0.427
E H    0.433
N H    0.418
V H     0.35
F C    0.372
S C    0.495
G C    0.479
W E    0.405
C E    0.438
V C    0.419
G C    0.534
N C    0.551
Y C    0.436
V E    0.437
S C    0.414
T C    0.447
Q C    0.554
G C    0.562
L E    0.441
S E    0.548
V E      0.6
H E    0.616
V E    0.576
R E    0.525
P E    0.545
V E    0.641
I E    0.665
L E    0.643
K E    0.519
R C    0.503
N C    0.681
S C    0.688
S C    0.614
A C    0.512
Q E    0.414
Y E    0.553
S E    0.576
V E    0.561
Q E    0.526
K E    0.473
T C    0.455
S C    0.482
I C    0.475
G C    0.482
S E    0.443
I E     0.55
R E    0.562
M E    0.498
R C    0.497
P C      0.6
Y C     0.68
N C    0.732
G C    0.727
S C    0.763
S C    0.732
END


