PFRMAT SS
TARGET T0107
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0107
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-23342/target-align-23342.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 12.5197
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0107
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.23056/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 Jul 10 12:31:12 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-23342/target-align-23342.a2m
METHOD 
METHOD  guide seq name: T0107
METHOD ###end 0
MODEL 1
V C    0.522
A C    0.493
T C    0.473
A C    0.443
K C    0.443
Y C    0.503
G C    0.647
T C    0.684
P C    0.629
V C    0.489
I C    0.459
D C    0.549
G C    0.547
E C    0.541
I C    0.414
D H    0.499
E H    0.563
I H    0.545
W H    0.562
N H    0.514
T H    0.445
T C      0.5
E C     0.49
E C     0.44
I C    0.357
E E     0.37
R E    0.382
K C    0.377
A E    0.467
V E    0.518
A E    0.504
M E    0.442
G C    0.462
S C    0.515
L C    0.528
D C     0.56
K C    0.597
N C    0.607
A C    0.435
T E    0.425
A E    0.461
K E    0.484
V E    0.514
R E    0.533
V E    0.559
L E    0.545
W E     0.49
D C    0.431
E C    0.577
N C    0.579
Y E    0.406
L E    0.604
Y E    0.661
V E    0.688
L E    0.679
A E     0.65
I E    0.625
V E    0.569
K C    0.467
D C    0.619
P C    0.618
V C    0.585
L C    0.555
N C    0.599
K C     0.58
D C    0.642
N C    0.682
S C    0.668
N C    0.713
P C    0.666
W C    0.616
E C    0.594
Q C    0.599
D C    0.585
S E    0.403
V E    0.599
E E    0.656
I E     0.72
F E     0.71
I E    0.644
D E    0.424
E C    0.632
N C    0.691
N C    0.689
H C    0.685
K C    0.639
T C    0.637
G C    0.626
Y C    0.579
Y C    0.556
E C    0.637
D C    0.673
D C    0.678
D C    0.659
A C    0.512
Q E    0.498
F E    0.643
R E    0.683
V E    0.678
N E    0.556
Y E    0.441
M C    0.593
N C    0.665
E C    0.577
Q C    0.442
T C    0.475
F C    0.544
G C    0.671
T C    0.651
G C    0.625
G C    0.536
S C    0.503
P C    0.408
A H    0.417
R H    0.415
F H      0.5
K H    0.508
T H    0.515
A H    0.489
V H    0.435
K H    0.397
L H    0.351
I C    0.479
E C    0.589
G C     0.63
G C    0.603
Y E    0.596
I E    0.697
V E     0.69
E E    0.664
A E    0.642
A E    0.621
I E      0.6
K E    0.497
W E    0.409
K C    0.481
T C    0.505
I C    0.463
K C    0.444
P C    0.423
T C     0.48
P C    0.537
N C    0.606
T C    0.439
V E    0.551
I E    0.602
G E    0.573
F E    0.574
N E    0.588
I E    0.643
Q E    0.657
V E    0.635
N E    0.518
D C    0.486
A C    0.652
N C    0.696
E C    0.682
K C    0.731
G C      0.7
Q C    0.531
R E    0.532
V E    0.604
G E    0.619
I E    0.665
I E    0.668
S E    0.627
W E    0.574
S C     0.46
D C    0.581
P C    0.656
T C    0.694
N C    0.728
N C    0.691
S C    0.608
W C    0.544
R C    0.547
D C    0.608
P C    0.554
S C    0.525
K C    0.473
F C    0.428
G C    0.428
N E    0.489
L E    0.578
R E    0.589
L E    0.556
I C    0.445
K C    0.619
END