
PFRMAT SS
TARGET T0122
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0122
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-9174/target-align-9174.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 105.481
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0122
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.6/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 03:15:17 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-9174/target-align-9174.a2m
METHOD 
METHOD  guide seq name: T0122
METHOD ###end 0
MODEL 1
M C    0.519
F C    0.469
K C    0.515
D C    0.563
G C    0.532
S E    0.491
L E    0.601
I E    0.592
P E    0.525
Y E    0.507
L E    0.494
T E    0.428
A C    0.465
G C    0.638
D C    0.724
P C     0.58
D C    0.599
K H    0.463
Q H    0.472
S H    0.492
T H    0.592
L H    0.743
N H    0.765
F H    0.772
L H    0.778
L H    0.768
A H    0.761
L H    0.751
D H    0.733
E H    0.602
Y C    0.649
A C    0.624
G C    0.461
A E    0.575
I E    0.617
E E      0.6
L E    0.537
G C    0.621
I C    0.678
P C     0.67
F C    0.583
S C    0.645
D C    0.752
P C    0.648
I C    0.522
A C    0.548
D C    0.603
G C    0.672
K C    0.477
T H    0.503
I H     0.57
Q H    0.617
E H    0.653
S H    0.657
H H    0.598
Y H      0.7
R H    0.688
A H    0.681
L H    0.673
K H    0.593
N H    0.474
G C    0.567
F C    0.586
K C    0.589
L H    0.554
R H    0.615
E H    0.642
A H    0.677
F H    0.737
W H    0.749
I H    0.749
V H    0.761
K H    0.766
E H     0.76
F H    0.737
R H    0.715
R H    0.683
H H    0.587
S C    0.499
S C    0.655
T C    0.649
P C    0.557
I E    0.594
V E     0.63
L E    0.608
M E    0.535
T E    0.408
Y C    0.412
Y C    0.441
N C    0.523
P C    0.416
I H    0.503
Y H    0.545
R H    0.547
A H    0.514
G C    0.534
V H    0.587
R H    0.682
N H    0.731
F H    0.742
L H    0.785
A H    0.792
E H    0.793
A H    0.794
K H    0.783
A H    0.761
S H    0.618
G C    0.683
V C    0.715
D C    0.647
G E     0.62
I E    0.705
L E    0.724
V E    0.659
V E     0.43
D C    0.589
L C    0.628
P C    0.654
V C    0.538
F C    0.509
H C    0.474
A H    0.646
K H    0.703
E H    0.725
F H    0.736
T H    0.753
E H    0.766
I H    0.765
A H    0.763
R H    0.754
E H    0.733
E H    0.583
G C    0.676
I C     0.67
K C    0.534
T E    0.563
V E    0.663
F E    0.674
L E    0.661
A E    0.507
A C    0.609
P C    0.673
N C    0.678
T C    0.689
P H    0.568
D H    0.694
E H    0.719
R H    0.734
L H    0.749
K H    0.748
V H    0.741
I H    0.726
D H    0.709
D H    0.671
M H    0.548
T C    0.606
T C     0.61
G C    0.563
F E    0.559
V E    0.661
Y E    0.679
L E    0.664
V E    0.591
S E    0.447
L C     0.47
Y C    0.564
G C    0.602
T C    0.578
T C    0.585
G C    0.557
A C    0.516
R C     0.46
E C    0.475
E C    0.507
I C    0.547
P C    0.543
K H    0.613
T H    0.633
A H    0.701
Y H    0.727
D H    0.746
L H    0.752
L H    0.773
R H    0.779
R H     0.77
A H    0.763
K H    0.744
R H    0.722
I H    0.655
C H    0.508
R C    0.619
N C    0.609
K C    0.432
V E    0.632
A E    0.646
V E    0.586
G E    0.446
F C     0.58
G C    0.654
V C    0.659
S C    0.693
K C    0.671
R H    0.644
E H    0.694
H H    0.707
V H    0.764
V H    0.773
S H    0.774
L H    0.768
L H    0.751
K H    0.725
E H    0.618
G C    0.687
A C    0.689
N C    0.611
G E    0.597
V E    0.668
V E    0.702
V E    0.649
G E    0.403
S H    0.517
A H    0.606
L H    0.619
V H    0.626
K H    0.619
I H    0.659
I H    0.665
G H    0.569
E H    0.566
K H    0.513
G H    0.542
R H    0.688
E H    0.721
A H    0.753
T H    0.768
E H    0.778
F H    0.777
L H    0.784
K H    0.786
K H    0.791
K H    0.789
V H    0.748
E H     0.73
E H    0.671
L H    0.591
L H    0.489
G C    0.556
I C    0.706
END


