
PFRMAT SS
TARGET T0090
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0090
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-21975/target-align-21975.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 78.239
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0090
METHOD  model_file: ./tmp.alpha.5886/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: Fri May 19 15:21:14 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-21975/target-align-21975.a2m
METHOD 
METHOD  guide seq name: T0090
METHOD ###end 0
MODEL 1
M C    0.609
L C    0.573
K C     0.59
P C    0.533
D C    0.516
N C    0.507
L C    0.504
P C    0.471
V C     0.44
T C     0.42
F C    0.444
G C    0.491
K C     0.47
N C    0.503
D C    0.494
V H    0.403
E H    0.415
I H    0.413
I H    0.412
A H    0.416
R H    0.391
E C      0.4
T C    0.413
L C    0.447
Y C     0.49
R C     0.52
G C    0.562
F C    0.579
F C    0.536
S C    0.424
L C    0.398
D C    0.402
L C    0.366
Y C     0.36
R E     0.37
F E    0.367
R E    0.369
H E    0.382
R C    0.411
L C    0.513
F C    0.583
N C    0.643
G C    0.591
Q C    0.518
M C    0.403
S C    0.373
H E    0.342
E E    0.359
V E    0.372
R E    0.378
R E    0.396
E E    0.402
I E    0.376
F C    0.424
E C     0.51
R C    0.583
G C    0.602
H C    0.594
A C    0.397
A E    0.565
V E    0.648
L E    0.686
L E    0.681
P E    0.651
F E    0.598
D E    0.426
P C    0.613
V C    0.646
R C    0.635
D C    0.594
E E    0.461
V E    0.637
V E    0.661
L E    0.653
I E    0.598
E E     0.52
Q E    0.415
I C    0.458
R C    0.562
I C    0.627
A C    0.577
A C    0.502
Y C    0.465
D C     0.62
T C    0.635
S C    0.648
E C    0.621
T C    0.621
P C      0.6
W C    0.486
L E     0.48
L E    0.541
E E    0.521
M E    0.425
V C    0.521
A C    0.534
G C     0.52
M C    0.445
I C    0.445
E C    0.605
E C    0.606
G C     0.64
E C    0.592
S C    0.553
V H    0.692
E H    0.728
D H    0.786
V H    0.811
A H    0.817
R H    0.832
R H    0.853
E H    0.854
A H     0.84
I H    0.841
E H    0.841
E H    0.805
A H    0.694
G C    0.654
L C    0.685
I C    0.561
V C     0.43
K H    0.379
R H    0.351
T E    0.396
K E    0.447
P E     0.46
V E     0.45
L E    0.415
S E    0.374
F C    0.386
L C    0.445
A C    0.534
S C    0.634
P C    0.651
G C     0.64
G C    0.608
T C    0.571
S C    0.519
E C    0.385
R E    0.518
S E    0.578
S E    0.624
I E    0.645
M E    0.654
V E    0.637
G E    0.588
E E    0.528
V E    0.419
D C    0.535
A C    0.617
T C    0.637
T C    0.548
A C    0.512
S C    0.522
G C    0.581
I C    0.591
H C    0.615
G C    0.605
L C    0.579
A C    0.608
D C    0.707
E C    0.599
N C    0.527
E C    0.432
D H    0.404
I H     0.37
R E    0.375
V E    0.408
H E    0.463
V E     0.47
V C    0.381
S C     0.59
R H    0.657
E H    0.707
Q H    0.716
A H    0.643
Y H     0.65
Q H    0.676
W H    0.653
V H    0.624
E H    0.582
E H    0.532
G H    0.478
K H    0.471
I H    0.499
D H     0.49
N H    0.472
A H    0.487
A H    0.535
S H    0.602
V H    0.658
I H    0.686
A H      0.7
L H    0.712
Q H    0.702
W H    0.703
L H    0.698
Q H    0.704
L H    0.683
H H    0.659
H H    0.625
Q H    0.635
A H    0.621
L H    0.602
K H     0.55
N H    0.457
E C    0.469
W C    0.475
A C    0.563
END


