PFRMAT SS
TARGET T0092
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0092
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-alpha-18638/target-align-18638.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 75.4612
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0092
METHOD  model_file: ./tmp.alpha.21963/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: Sat May 20 12:29:29 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-18638/target-align-18638.a2m
METHOD 
METHOD  guide seq name: T0092
METHOD ###end 0
MODEL 1
M C      0.6
V C     0.52
K C    0.447
D H    0.471
T H    0.484
L H    0.467
F H    0.435
S H    0.478
T H    0.487
P H     0.51
I H    0.566
A H     0.62
K H    0.614
L H    0.591
G H     0.55
D H    0.534
F H    0.483
I H     0.45
F H    0.399
D C    0.504
E C    0.468
N C    0.494
V H    0.436
A H    0.454
E H    0.445
V H    0.414
F C    0.427
P H    0.429
D H     0.44
M H    0.493
I H    0.481
Q H    0.486
R H    0.474
S H    0.443
V H    0.427
P H    0.424
G H    0.443
Y H    0.447
S H    0.484
N H    0.529
I H      0.6
I H    0.634
T H    0.659
A H    0.711
I H    0.723
G H    0.725
M H    0.723
L H    0.719
A H    0.684
E H    0.645
R H    0.534
F C    0.522
V C    0.526
T C    0.613
A C    0.644
D C    0.619
S C    0.528
N E    0.528
V E     0.62
Y E    0.596
D E    0.495
L C    0.439
G C    0.604
C C    0.681
S C    0.656
R C    0.469
G H    0.504
A H     0.59
A H    0.627
T H    0.669
L H    0.686
S H    0.692
A H    0.702
R H    0.707
R H    0.685
N H    0.636
I H    0.494
N C    0.603
Q C     0.68
P C    0.656
N C    0.615
V C    0.491
K E    0.557
I E    0.669
I E     0.68
G E    0.635
I E    0.561
D C     0.49
N C     0.63
S C    0.659
Q H    0.743
P H    0.771
M H    0.783
V H    0.821
E H    0.832
R H    0.839
C H    0.829
R H    0.827
Q H    0.811
H H    0.789
I H    0.764
A H    0.734
A H    0.686
Y H    0.503
H C     0.64
S C    0.632
E C    0.579
I C    0.555
P C    0.534
V E    0.424
E E     0.53
I E    0.571
L E    0.551
C E    0.491
N C    0.395
D C    0.551
I C    0.429
R H    0.404
H C    0.417
V C      0.5
E C    0.573
I C    0.581
K C    0.634
N C    0.604
A C    0.549
S C    0.476
M E    0.597
V E    0.635
I E    0.622
L E    0.563
N H    0.389
F H    0.437
T H    0.467
L H    0.485
Q H     0.43
F C    0.451
L C    0.596
P C      0.7
P H    0.608
E H    0.673
D H    0.658
R H    0.766
I H    0.808
A H    0.827
L H    0.828
L H    0.833
T H    0.839
K H    0.833
I H    0.823
Y H    0.786
E H    0.751
G H    0.695
L H    0.541
N C    0.641
P C    0.616
N C    0.698
G C    0.609
V E    0.548
L E    0.712
V E    0.731
L E    0.695
S E    0.588
E E    0.399
K C    0.473
F C    0.468
R C    0.533
F C    0.592
E C    0.576
D C    0.531
T C    0.509
K C    0.471
I H    0.464
N H    0.509
H H    0.558
L H     0.56
L H    0.556
I H    0.559
D H    0.593
L H    0.584
H H     0.56
H H    0.531
Q H    0.483
F H    0.389
K C    0.367
R C    0.404
A C    0.442
N C    0.502
G C    0.594
Y C    0.609
S C    0.577
E C    0.497
L C    0.441
E C    0.411
V H    0.444
S H    0.469
Q H    0.509
K H    0.489
R H    0.475
T H    0.435
A H    0.394
L C    0.467
E C    0.521
N C    0.556
V C    0.524
M C    0.535
R C    0.514
T C    0.541
D C     0.58
S C    0.648
I H    0.737
E H    0.793
T H    0.803
H H    0.824
K H    0.831
V H    0.839
R H    0.836
L H    0.836
K H    0.821
N H    0.811
V H    0.658
G C    0.686
F C    0.705
S C    0.437
Q E    0.488
V E    0.493
E E    0.468
L E    0.434
W C    0.349
F C    0.426
Q C    0.454
C C    0.461
F C    0.446
N C     0.42
F H    0.371
G H    0.375
S H    0.391
M H    0.382
I H    0.418
A H    0.406
V C    0.378
K C     0.53
END