PFRMAT SS
TARGET T0086
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0086
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-27626/target-align-27626.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 4.70987
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0086
METHOD  model_file: ./tmp.alpha.20268/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 May  9 11:23:36 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-27626/target-align-27626.a2m
METHOD 
METHOD  guide seq name: T0086
METHOD ###end 0
MODEL 1
S C     0.65
H C    0.619
P C      0.5
A H    0.502
L H    0.575
T H    0.562
Q H    0.571
L H    0.483
R H    0.469
A H    0.489
L C    0.462
R C    0.443
Y H    0.479
C H    0.477
K H    0.485
E H    0.446
I C    0.448
P C    0.533
A C    0.509
L C    0.575
D C    0.657
P C    0.557
Q C    0.503
L H    0.462
L H    0.606
D H    0.636
W H    0.673
L H    0.645
L H    0.569
L H    0.503
E H    0.617
D H    0.662
S H    0.679
M H    0.747
T H    0.755
K H    0.807
R H    0.799
F H    0.786
E H    0.731
Q H    0.625
Q C     0.51
G C     0.64
K C    0.626
T C    0.427
V E    0.513
S E    0.566
V E    0.585
T E    0.563
M E    0.537
I E     0.48
R E    0.382
E C    0.405
G C    0.537
F C    0.482
V C    0.466
E C    0.543
Q C    0.592
N C    0.589
E C    0.546
I C    0.524
P C    0.443
E H    0.477
E H    0.454
L C    0.554
P C    0.592
L C    0.614
L C    0.636
P C    0.662
K C    0.551
E C    0.518
S C    0.476
R H    0.479
Y H    0.513
W H    0.554
L H    0.591
R H    0.607
E H    0.609
I H     0.58
L H    0.586
L H    0.583
C H    0.485
A C    0.492
D C    0.668
G C    0.754
E C    0.727
P C    0.517
W E    0.538
L E    0.558
A E    0.509
G E    0.438
R E    0.405
T E    0.489
V E    0.526
V E    0.496
P E    0.419
V C    0.388
S C    0.445
T C    0.514
L C    0.533
S C    0.574
G C    0.461
P H    0.535
E H    0.681
L H    0.722
A H    0.711
L H    0.714
Q H    0.644
K H    0.596
L C     0.48
G C     0.73
K C     0.76
T C    0.705
P C    0.636
L C     0.58
G C    0.542
R C    0.449
Y H    0.396
L H    0.372
F C     0.42
T C    0.547
S C    0.587
S C    0.633
T C    0.573
L C    0.568
T C    0.512
R C    0.415
D C    0.368
F E    0.424
I E     0.51
E E    0.529
I E    0.477
G C    0.501
R C    0.574
D C    0.609
A C    0.529
G C    0.478
L H    0.457
W H    0.452
G H     0.47
R H    0.482
R H    0.544
S H    0.542
R H    0.533
L H    0.488
R H    0.452
L H    0.486
S C    0.514
G C    0.576
K C    0.553
P H    0.382
L E    0.421
L E     0.45
L H    0.442
T H    0.508
E H     0.54
L H    0.478
F C    0.445
L C    0.561
P C     0.52
A C    0.494
S C    0.491
P C    0.489
L C    0.479
Y C    0.557
END