PFRMAT SS
TARGET T0123
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0123
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-9643/target-align-9643.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 113.494
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0123
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.19747/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: Sun Aug 20 02:55:05 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-9643/target-align-9643.a2m
METHOD 
METHOD  guide seq name: T0123
METHOD ###end 0
MODEL 1
V C    0.574
E C     0.62
V C    0.585
T C    0.588
P C    0.576
I C    0.528
M C     0.56
T C    0.606
E C    0.635
L C    0.637
D C    0.665
T H    0.568
Q H     0.57
K H    0.606
V H    0.524
A C    0.412
G C    0.455
T C    0.385
W E    0.448
H E    0.535
T E    0.551
V E    0.552
A E    0.519
M E     0.49
A E    0.422
V C    0.495
S C    0.638
D C    0.582
V C    0.478
S C    0.425
L C    0.375
L C    0.366
D C    0.406
A C    0.446
K C    0.504
S C    0.563
S C    0.632
P C    0.553
L C    0.455
K C    0.418
A E    0.458
Y E    0.556
V E    0.579
E E    0.586
G E    0.598
L E    0.602
K E    0.562
P E    0.513
T C    0.486
P C    0.639
E C    0.648
G C    0.632
D C    0.522
L E    0.534
E E    0.582
I E    0.617
L E    0.614
L E     0.61
Q E    0.596
K E    0.562
R E    0.475
E C    0.415
N C    0.595
D C    0.614
K C    0.498
C E    0.441
A E    0.529
Q E    0.551
E E    0.582
V E    0.617
L E    0.628
L E    0.627
A E    0.585
K E      0.5
K E    0.423
T C    0.561
D C    0.662
I C    0.744
P C    0.707
A C    0.521
V E     0.53
F E    0.668
K E    0.674
I E    0.647
N E    0.529
A E    0.418
L C    0.546
D C    0.634
E C    0.623
N C    0.525
Q E    0.555
L E    0.666
F E    0.719
L E    0.714
L E    0.656
D E    0.534
T C    0.463
D C    0.636
Y C    0.535
D C    0.502
S C    0.422
H E     0.52
L E    0.655
L E    0.686
L E    0.683
C E    0.656
M E    0.588
E E    0.462
N C    0.455
S C    0.475
A C    0.583
S C    0.685
P C    0.679
E C     0.58
H E    0.414
S E    0.539
L E     0.58
V E    0.599
C E      0.6
Q E    0.597
S E    0.591
L E    0.553
A E    0.462
R C    0.485
T C    0.615
L C    0.571
E C     0.61
V C    0.605
D C    0.639
D H    0.723
Q H    0.748
I H    0.766
R H    0.801
E H    0.823
K H    0.824
F H    0.818
E H    0.816
D H     0.82
A H    0.804
L H     0.79
K H    0.775
T H    0.753
L H    0.593
S C     0.68
V C    0.702
P C     0.66
M H    0.475
R H    0.514
I H    0.442
L E     0.38
P E     0.44
A C     0.41
Q C    0.533
L C    0.568
E C    0.584
E C     0.57
Q C    0.552
C C    0.568
R C    0.627
V C    0.753
END