
PFRMAT SS
TARGET T0108
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0108
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-8895/target-align-8895.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 6.45715
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0108
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.12757/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 13:04:00 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-8895/target-align-8895.a2m
METHOD 
METHOD  guide seq name: T0108
METHOD ###end 0
MODEL 1
M C    0.516
G C    0.569
A C    0.592
S C    0.646
G H    0.484
Q H    0.512
Y H    0.512
V H    0.458
R H    0.457
A H    0.415
R H    0.406
I H    0.401
K H    0.377
G C    0.531
A C    0.514
Y C    0.522
Y C    0.475
A C    0.449
T C    0.414
P C    0.454
V C    0.492
D C    0.481
P C    0.476
V C     0.43
T C    0.481
N C    0.591
Q C    0.701
P C    0.694
T C    0.647
A C    0.645
P C    0.531
K C    0.466
D C    0.419
F C    0.509
S C     0.51
S H    0.401
G H    0.411
F E    0.378
W E    0.404
D C    0.414
F C    0.455
N C    0.592
D C    0.662
G C    0.699
T C    0.576
T C    0.507
Q C    0.536
G C    0.579
F C    0.504
G C    0.485
V C    0.513
N C    0.643
P C    0.696
D C      0.7
S C    0.707
P C    0.687
I C    0.575
T C    0.474
A E    0.442
I E    0.573
N E     0.59
V E    0.574
E E    0.479
N C    0.399
A C    0.479
N C    0.585
N C    0.553
A C    0.412
L H    0.377
K H    0.375
I H    0.425
S C    0.412
N C    0.619
L C    0.607
N C    0.655
S C     0.61
K C    0.603
G C    0.644
S C     0.61
N C    0.552
D C    0.517
L C    0.477
S C    0.538
E C    0.521
G C    0.557
N C    0.628
F C     0.54
W C     0.41
A E    0.384
N E    0.383
V E    0.378
R C    0.414
I C    0.421
S C    0.513
A C    0.595
D C    0.656
I C    0.627
W C    0.556
G C      0.4
Q E    0.475
S E    0.541
I E    0.568
N E    0.539
I E    0.545
Y E    0.404
G C    0.592
D C    0.517
T C    0.451
K C    0.393
L C    0.394
T E    0.409
M E    0.452
D C    0.509
V E    0.416
I E    0.454
A C    0.411
P C    0.552
T C    0.647
P C    0.626
V C    0.483
N E    0.501
V E    0.627
S E    0.649
I E    0.664
A E    0.617
A E    0.592
I E    0.501
P C    0.484
Q C     0.63
S C    0.748
S C    0.719
T C    0.673
H C    0.643
G C    0.642
W C    0.531
G C    0.499
N C    0.579
P C    0.597
T C    0.613
R C    0.533
A E    0.402
R E    0.533
I E    0.582
V E    0.556
W C    0.469
T H    0.404
N H    0.445
N H    0.454
F H    0.387
V C    0.341
A C    0.379
Q C    0.506
T C     0.61
D C    0.658
G C    0.594
T E    0.417
Y E    0.575
K E    0.614
A E    0.649
T E    0.668
L E    0.679
T E    0.677
I E    0.626
S E    0.446
T C    0.543
N C    0.592
D C    0.609
S C    0.547
P C    0.502
N C     0.47
F C    0.437
N C    0.467
T C    0.442
I C    0.429
A C    0.423
T C    0.447
D C    0.537
A C    0.583
A C    0.579
D C     0.59
S C    0.443
V C    0.341
V E    0.389
T C    0.364
N E    0.406
M E    0.616
I E    0.685
L E      0.7
F E    0.683
V E    0.584
G C    0.417
S C    0.628
N C    0.655
S C     0.64
D C    0.619
N E      0.5
I E     0.63
S E    0.622
L E    0.572
D E    0.416
N C    0.438
I E    0.461
K E    0.538
F E    0.519
T C     0.46
K C    0.785
END


