
PFRMAT SS
TARGET T0109
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0109
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-7224/target-align-7224.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 22.6274
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0109
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.24160/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: Mon Jul 10 13:09:07 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-7224/target-align-7224.a2m
METHOD 
METHOD  guide seq name: T0109
METHOD ###end 0
MODEL 1
M C     0.67
S C    0.617
F C    0.535
D C    0.543
K C    0.542
Q C    0.484
N E    0.415
L E    0.613
I E    0.667
W E    0.664
I E    0.614
D C    0.422
L C    0.462
E C    0.459
M C    0.459
T C     0.59
G C    0.716
L C    0.706
D C     0.72
P H    0.491
E H    0.534
K H    0.596
E H    0.575
R H    0.563
I H    0.536
I E    0.478
E E    0.521
I E    0.568
A E    0.582
T E    0.597
I E     0.62
V E    0.594
T E    0.473
D C    0.498
K C    0.595
N C    0.583
L C    0.425
N C     0.38
I H    0.363
L H    0.376
A C    0.449
E C    0.492
G C    0.642
P C    0.571
V C    0.466
L E    0.529
A E    0.567
V E    0.522
H E    0.385
Q C    0.444
S H    0.427
D H    0.524
E H    0.535
L H    0.469
L H      0.4
N C    0.552
K C    0.494
M C    0.506
N C    0.503
D C    0.497
W C    0.479
C C    0.507
Q H    0.617
K H     0.62
T H    0.619
H H    0.575
S H    0.549
E H    0.536
N H    0.454
G C    0.578
L C    0.549
I C    0.545
E H    0.586
R H    0.613
I H    0.598
K H    0.562
A H    0.499
S C    0.511
K C    0.599
L C    0.594
T C    0.575
E H    0.722
R H     0.76
A H    0.787
A H    0.783
E H    0.792
L H    0.804
Q H    0.803
T H    0.801
L H    0.795
D H    0.788
F H     0.77
L H    0.739
K H    0.685
K H    0.634
W H     0.52
V C    0.501
P C    0.597
K C     0.64
G C    0.665
A C    0.645
S C    0.601
P E    0.433
I E    0.549
C E    0.521
G E    0.397
N C    0.528
S C    0.527
I C    0.521
A C    0.461
Q H    0.484
D H    0.544
K H    0.679
R H    0.684
F H    0.688
L H    0.686
V H    0.689
K H     0.69
Y H    0.666
M H    0.567
P H    0.574
D H    0.543
L H    0.499
A C    0.448
D H    0.442
Y H    0.432
F C    0.431
H C    0.468
Y C    0.459
R C    0.441
H C    0.383
L C    0.418
D C    0.443
V H    0.411
S H    0.416
T H    0.436
L H    0.698
K H    0.741
E H    0.743
L H    0.733
A H    0.719
A H    0.696
R H    0.646
W H    0.526
K C      0.6
P C    0.461
E H    0.549
I H    0.567
L H    0.537
E H    0.447
G C    0.578
F C    0.591
K C    0.595
K C    0.521
E C    0.512
N C    0.486
T H    0.463
H H    0.606
L H    0.634
A H     0.64
L H    0.688
D H    0.704
D H    0.714
I H    0.756
R H    0.752
E H    0.747
S H    0.738
I H    0.786
K H    0.794
E H    0.792
L H    0.793
A H    0.781
Y H    0.774
Y H    0.761
R H    0.757
E H    0.738
H H    0.704
F H    0.595
M H    0.496
K C    0.475
L C    0.561
D C    0.682
END


