PFRMAT SS
TARGET T0125
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0125
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-4567/target-align-4567.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 5.59869
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0125
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.23369/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: Wed Aug 23 11:32:15 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-4567/target-align-4567.a2m
METHOD 
METHOD  guide seq name: T0125
METHOD ###end 0
MODEL 1
F C    0.616
D C    0.656
D C    0.597
V E    0.414
V E    0.498
V E    0.481
S C     0.45
R H    0.475
Q H    0.565
E H    0.633
Q H    0.771
S H    0.783
Y H    0.781
V H    0.775
Q H     0.79
R H    0.785
G H     0.77
M H    0.763
V H    0.772
N H    0.771
F H    0.755
L H    0.719
D H     0.67
E H    0.762
E H    0.761
M H     0.77
H H    0.771
K H    0.778
L H    0.777
V H    0.781
K H    0.781
R H    0.763
F H    0.748
R H    0.728
D H    0.674
M H    0.514
R C    0.632
W C    0.583
N C    0.578
L C    0.581
G C    0.713
P C    0.681
G C    0.617
F C    0.506
V H    0.399
F H    0.444
L H    0.486
L H    0.537
K H    0.548
K H    0.572
V H     0.57
N H    0.573
R H     0.75
E H     0.78
R H    0.778
M H    0.762
M H    0.743
R H    0.741
Y H    0.714
C H    0.675
M H    0.658
D H    0.645
Y H     0.65
A H     0.64
R H    0.636
Y H    0.621
S H    0.612
K H    0.626
K H    0.604
I H    0.572
L H    0.579
Q H    0.561
L H    0.524
K C    0.461
H C     0.56
L C    0.623
P C    0.611
V C    0.563
N C    0.616
K H    0.655
K H    0.675
T H    0.673
L H    0.713
T H    0.716
K H     0.72
M H     0.66
G H    0.504
R H    0.488
F H    0.473
V H    0.475
G H    0.436
Y H    0.437
R H    0.456
N H      0.5
Y H    0.568
G H    0.568
V H    0.613
I H    0.684
R H    0.722
E H    0.725
L H    0.705
Y H    0.666
A H    0.623
D H    0.584
V H    0.544
F H    0.505
R H    0.503
D H    0.473
V H    0.445
Q H    0.424
G H    0.393
F C     0.44
R C    0.526
G C    0.551
P C    0.476
K H    0.491
M H    0.541
T H    0.596
A H    0.681
A H    0.678
M H    0.701
R H    0.694
K H     0.67
Y H    0.613
S H    0.515
S C    0.448
K C     0.54
D C    0.637
P C    0.631
G C     0.66
T C    0.677
F C    0.697
P C    0.733
C C    0.743
K C    0.721
N C    0.597
E C    0.542
K C    0.514
R C     0.52
R C     0.62
G C    0.787
END