PFRMAT SS
TARGET T0118
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0118
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-11351/target-align-11351.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 2.1277
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0118
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.19800/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: Thu Jul 27 05:26:32 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-11351/target-align-11351.a2m
METHOD 
METHOD  guide seq name: T0118
METHOD ###end 0
MODEL 1
M C    0.667
A C    0.595
G C    0.573
Y C    0.493
G C    0.462
A H    0.427
K C     0.44
G C    0.433
I H    0.406
R H    0.426
K H    0.473
V H     0.46
G H     0.45
A H     0.48
F H    0.502
R H    0.531
S H    0.456
G C    0.505
L C    0.477
E H    0.531
D H    0.619
K H    0.631
V H    0.657
S H    0.673
K H    0.726
Q H    0.712
L H    0.722
E H    0.693
S H    0.647
K C    0.456
G C    0.677
I C     0.58
K E    0.443
F E    0.572
E E    0.517
Y E     0.47
E E    0.408
E E    0.404
W E    0.414
K E    0.422
V C    0.505
P C    0.545
Y E    0.631
V E    0.681
I E    0.566
P C    0.524
A C    0.645
S C    0.654
N C     0.66
H C    0.599
T C    0.468
Y C    0.504
T C    0.653
P C    0.637
D C    0.562
F E    0.441
L E     0.48
L C    0.476
P C    0.662
N C    0.683
G C    0.542
I E    0.568
F E    0.644
V E    0.634
E E    0.526
T C    0.415
K C    0.528
G C    0.562
L C    0.535
W C    0.578
E C    0.608
S C    0.588
D C    0.517
D C    0.517
R H    0.523
K H    0.531
K H    0.549
H H    0.484
L H    0.461
L H    0.508
I H    0.479
R H     0.46
E C    0.429
Q C    0.522
H C    0.729
P C    0.583
E C    0.457
L C    0.428
D C    0.482
I E    0.461
R E    0.583
I E    0.663
V E    0.665
F E    0.629
S E    0.406
S C    0.572
S C    0.633
R H    0.473
T H    0.468
K H    0.467
L H      0.4
Y C     0.38
K C    0.521
G C    0.679
S C    0.773
P C    0.709
T C    0.643
S C    0.577
Y C    0.458
G C    0.429
E H    0.431
F H    0.462
C H    0.515
E H    0.527
K H    0.544
H H    0.465
G C    0.515
I C    0.438
K H     0.35
F H    0.468
A H    0.489
D H    0.498
K H    0.427
L C    0.394
I C    0.502
P C    0.547
A H    0.454
E H    0.467
W H    0.435
I C    0.422
K C    0.502
E C    0.675
P C    0.699
K C    0.639
K C    0.581
E C    0.568
V C    0.637
P C    0.672
F H      0.5
D H    0.542
R H     0.57
L H    0.512
K H    0.445
R C    0.437
K C    0.527
G C     0.64
G C    0.703
K C    0.686
K C      0.7
END