
PFRMAT SS
TARGET T0098
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0098
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-1396/target-align-1396.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 3.47416
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0098
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.alpha.9128/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: Mon Jun 12 10:52:55 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-1396/target-align-1396.a2m
METHOD 
METHOD  guide seq name: T0098
METHOD ###end 0
MODEL 1
D C    0.702
N C    0.648
K C    0.622
P C    0.564
K C    0.513
N C     0.48
L C    0.457
D H    0.435
A H    0.532
S H    0.566
I H    0.629
T H    0.639
S H    0.647
I H    0.638
I H     0.64
H H    0.641
E H    0.634
I H    0.566
G C    0.639
V C    0.622
P C    0.577
A H    0.421
H H    0.491
I H    0.533
K H    0.569
G H    0.575
Y H    0.618
L H    0.639
Y H    0.653
L H     0.68
R H    0.706
E H    0.716
A H    0.703
I H    0.683
A H    0.665
M H     0.65
V H     0.62
Y H    0.621
H H    0.604
D H    0.583
I H    0.671
E H    0.677
L H    0.682
L H    0.671
G H    0.657
S H    0.658
I H    0.657
T H    0.659
K H    0.688
V H    0.661
L H    0.645
Y H    0.586
P H    0.697
D H    0.733
I H    0.743
A H    0.732
K H    0.733
K H    0.704
Y H    0.644
N C     0.54
T C    0.554
T C    0.546
A H    0.666
S H    0.699
R H    0.726
V H    0.755
E H    0.774
R H    0.778
A H    0.767
I H     0.75
R H    0.695
H H    0.796
A H     0.77
I H    0.736
E H    0.694
V H    0.624
A H    0.605
W H    0.593
S H    0.533
R C    0.472
G C    0.655
N C      0.6
L H    0.501
E H    0.512
S H    0.534
I H    0.591
S H    0.589
S H    0.565
L H    0.511
F H    0.445
G C     0.52
Y C    0.446
T C     0.39
V C    0.389
S C    0.442
V C    0.471
S C    0.524
K C    0.577
A C    0.665
K C    0.739
P C    0.738
T C      0.7
N C    0.597
S H    0.511
E H    0.626
F H    0.652
I H    0.663
A H     0.67
M H     0.69
V H    0.678
A H    0.678
D H    0.668
K H    0.645
L H    0.603
R H    0.521
L H    0.509
E H    0.473
H H    0.458
K H     0.41
A C    0.485
S C    0.666
END


