
PFRMAT SS
TARGET T0128
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0128
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-11303/target-align-11303.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 35.5257
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0128
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.22366/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 Aug 29 23:16:16 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-11303/target-align-11303.a2m
METHOD 
METHOD  guide seq name: T0128
METHOD ###end 0
MODEL 1
M C    0.563
R C    0.551
G C    0.563
S C     0.52
H C    0.491
H C    0.453
H C    0.442
H C    0.423
H C    0.447
H C    0.452
G C    0.438
S C    0.417
V E    0.356
T E    0.413
T E    0.393
K C    0.405
R E    0.392
Y E    0.436
T E    0.407
L C    0.556
P C    0.667
P C    0.676
L C    0.672
P C    0.668
Y C    0.606
A C    0.629
Y C     0.45
N C    0.457
A C    0.442
L C    0.444
E C    0.505
P C    0.498
Y C     0.48
I C    0.479
S C    0.591
A H    0.698
E H    0.708
I H    0.703
M H    0.694
Q H    0.696
L H    0.673
H H    0.647
H H    0.647
Q H    0.666
K H    0.682
H H    0.679
H H    0.687
Q H    0.681
G H    0.673
Y H    0.665
V H    0.689
N H    0.695
G H    0.689
A H    0.717
N H    0.708
A H    0.727
A H    0.707
L H    0.716
E H    0.699
K H    0.665
L H    0.595
E H    0.619
K H    0.619
F H     0.55
R H    0.478
K C    0.485
G C    0.492
E H    0.507
A H    0.563
Q H    0.618
I H    0.613
D H    0.611
I H     0.61
R H    0.586
A H     0.55
V H    0.517
L H    0.533
R H    0.559
D H    0.557
L H    0.562
S H    0.552
F H    0.485
H C    0.467
L H    0.459
N H    0.493
G H    0.524
H H    0.537
I H    0.547
L H    0.549
H H    0.574
S H    0.587
I H    0.592
F H    0.565
W H     0.56
P H    0.552
N H    0.504
M C    0.416
A C    0.674
P C    0.705
P C    0.702
G C    0.675
K C    0.679
G C    0.722
G C     0.73
G C    0.721
K C    0.708
P C    0.693
G C    0.537
G H    0.649
K H    0.676
I H    0.708
A H    0.734
D H    0.746
L H    0.738
I H    0.726
N H    0.717
K H    0.721
F H    0.667
F H    0.549
G C    0.642
S C    0.654
F H    0.739
E H    0.768
K H     0.78
F H    0.775
K H    0.788
E H    0.798
E H    0.789
F H    0.776
S H    0.751
Q H    0.748
A H    0.705
A H    0.671
K H    0.622
N H    0.536
V C    0.433
E C    0.501
G C    0.622
V C    0.621
G C    0.519
W E    0.441
A E    0.565
I E    0.627
L E    0.646
V E    0.612
Y E    0.541
E C    0.467
P C    0.602
L C    0.605
E C    0.631
E C    0.607
Q C    0.382
L E    0.549
L E    0.604
I E    0.609
L E    0.565
Q E    0.478
I C    0.469
E C     0.58
K C     0.66
H C    0.664
N C    0.676
L C    0.666
M C     0.62
H C     0.52
A C    0.517
A C    0.574
D C    0.633
A C    0.618
Q C    0.453
V E    0.474
L E    0.588
L E    0.604
A E    0.573
L E     0.51
D C    0.395
V H    0.519
W H    0.602
E H    0.641
H H    0.657
A H    0.639
Y H     0.63
Y H    0.631
L H    0.617
Q H     0.58
Y H    0.559
K H    0.443
N C    0.598
D C    0.569
R C    0.534
G H    0.586
S H    0.656
Y H    0.667
V H    0.682
D H    0.688
N H    0.683
W H     0.67
W H    0.635
N H    0.603
V H    0.486
V C    0.405
N C    0.607
W H    0.693
D H    0.715
D H    0.734
V H     0.74
E H    0.744
R H    0.745
R H    0.734
L H    0.731
Q H    0.746
K H    0.735
A H    0.711
L H    0.693
N H     0.69
G H    0.642
Q H    0.577
I H    0.564
A H    0.545
L C    0.497
K C    0.531
L C    0.911
END


