PFRMAT SS
TARGET T0104
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0104
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-861/target-align-861.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 21.99
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0104
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.7877/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: Tue Jun 27 13:27:27 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-861/target-align-861.a2m
METHOD 
METHOD  guide seq name: T0104
METHOD ###end 0
MODEL 1
M C    0.614
E C    0.556
S C      0.5
L C    0.415
T H    0.384
Q H    0.386
Y H    0.373
I C    0.418
P C    0.473
D C    0.484
E H    0.639
F H    0.673
S H    0.688
M H    0.691
L H    0.723
R H     0.73
F H    0.734
G H    0.723
K H    0.744
K H    0.749
F H    0.744
A H    0.733
E H    0.717
I H    0.691
L H    0.658
L H    0.747
K H    0.709
L H    0.626
H C    0.442
T C     0.47
E C    0.599
K C    0.614
A C    0.616
I C    0.439
M E    0.647
V E     0.71
Y E    0.702
L E    0.636
N E    0.448
G C    0.593
D C     0.59
L C    0.548
G C    0.608
A C    0.565
G C      0.5
K H    0.515
T H    0.565
T H    0.617
L H    0.648
T H    0.664
R H    0.678
G H     0.68
M H     0.67
L H    0.675
Q H    0.649
G H    0.607
I H    0.498
G C    0.617
H C    0.649
Q C    0.592
G C    0.528
N C    0.494
V E    0.452
K C    0.471
S C    0.651
P C    0.551
T C    0.426
Y H    0.383
T E    0.436
L E    0.491
V E    0.493
E E    0.435
E E    0.384
Y C    0.416
N C    0.547
I C    0.583
A C    0.636
G C    0.612
K C    0.526
M E    0.413
I E     0.57
Y E    0.587
H E    0.572
F E     0.55
D E    0.488
L E     0.53
Y E    0.524
R E    0.464
L C    0.379
A C    0.535
D C    0.608
P H    0.552
E H    0.603
E H    0.605
L H    0.589
E H    0.585
F H     0.57
M H    0.509
G C    0.459
I H    0.533
R H    0.571
D H    0.574
Y H    0.541
F H    0.481
N C    0.447
T C    0.567
D C      0.6
S C    0.516
I E    0.551
C E    0.652
L E    0.667
I E    0.633
E E    0.508
W C    0.418
S C    0.534
E H     0.44
K H     0.48
G H    0.494
Q H    0.476
G C    0.421
I C    0.466
L C    0.611
P C    0.634
E C    0.545
A C    0.527
D C    0.411
I E     0.53
L E    0.592
V E    0.617
N E    0.621
I E    0.618
D E    0.587
Y E    0.506
Y C    0.514
D C    0.671
D C    0.692
A C    0.622
R C    0.451
N E    0.511
I E    0.575
E E    0.579
L E     0.57
I E    0.504
A E    0.452
Q E    0.372
T C    0.414
N C    0.469
L C    0.438
G H    0.429
K H      0.5
N H    0.517
I H     0.54
I H     0.53
S H    0.535
A H    0.541
F H    0.477
S H    0.405
N C    0.555
END