PFRMAT SS
TARGET T0096
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0096
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-18351/target-align-18351.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 72.1128
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0096
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.alpha.31762/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: Sat Jun 10 04:05:17 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-alpha-18351/target-align-18351.a2m
METHOD 
METHOD  guide seq name: T0096
METHOD ###end 0
MODEL 1
M C    0.691
V C    0.669
I C    0.607
K C     0.63
A C    0.614
Q C    0.596
S C    0.575
P H    0.635
A H    0.723
G H    0.765
F H    0.773
A H    0.775
E H      0.8
E H    0.818
Y H    0.806
I H    0.798
I H    0.794
E H    0.782
S H    0.749
I H    0.719
W H    0.678
N H    0.613
N C    0.625
R C    0.565
F C    0.569
P C    0.688
P C    0.691
G C    0.713
T C    0.676
I C    0.629
L C    0.677
P C    0.736
A C     0.63
E H    0.685
R H    0.731
E H    0.739
L H    0.754
S H    0.753
E H    0.754
L H    0.739
I H    0.664
G C    0.585
V C     0.63
T C    0.643
R H    0.678
T H    0.701
T H    0.729
L H    0.784
R H    0.822
E H    0.849
V H    0.842
L H    0.839
Q H    0.829
R H    0.822
L H    0.804
A H    0.775
R H    0.761
D H     0.68
G C    0.575
W C     0.42
L E    0.472
T E    0.534
I E    0.513
Q E    0.437
H C    0.489
G C    0.643
K C    0.578
P C    0.508
T E    0.504
K E    0.612
V E    0.574
N E    0.436
N C    0.576
F C    0.577
W C    0.546
E C    0.511
T C    0.525
S C    0.557
G C    0.576
L C     0.57
N C    0.588
I C    0.479
L C    0.431
E H    0.488
T H    0.527
L H    0.565
A H    0.572
R H    0.552
L H    0.509
D C    0.451
H C    0.447
E C    0.486
S C    0.532
V C    0.603
P H    0.479
Q H    0.527
L H    0.537
I H    0.675
D H    0.704
N H    0.716
L H    0.753
L H    0.765
S H    0.766
V H    0.763
R H    0.764
T H    0.761
N H    0.755
I H    0.759
S H    0.756
T H    0.759
I H     0.74
F H    0.752
I H    0.753
R H    0.754
T H    0.746
A H    0.727
F H    0.697
R H    0.635
Q H    0.487
H C    0.554
P C    0.646
D H    0.685
K H    0.728
A H     0.73
Q H     0.79
E H    0.794
V H    0.794
L H    0.798
A H    0.801
T H    0.797
A H    0.782
N H    0.768
E H    0.728
V H    0.704
A H    0.579
D C    0.566
H C    0.568
A H    0.577
D H    0.628
A H    0.658
F H    0.649
A H    0.637
E H     0.63
L H      0.6
D H    0.611
Y H    0.725
N H    0.728
I H    0.731
F H    0.724
R H    0.728
G H    0.723
L H     0.71
A H    0.697
F H    0.695
A H    0.677
S H    0.592
G H    0.534
N H    0.623
P H    0.691
I H    0.712
Y H    0.729
G H    0.745
L H    0.751
I H    0.751
L H    0.764
N H    0.764
G H    0.751
M H    0.738
K H    0.714
G H    0.702
L H    0.683
Y H    0.657
T H     0.63
R H    0.616
I H     0.58
G H    0.537
R H    0.514
H H    0.471
Y H    0.406
F C    0.449
A C    0.494
N C    0.548
P H    0.511
E H    0.571
A H    0.609
R H    0.646
S H    0.672
L H    0.677
A H    0.673
L H    0.721
G H    0.738
F H    0.736
Y H    0.751
H H    0.755
K H    0.751
L H     0.74
S H    0.739
A H    0.744
L H    0.742
C H     0.72
S H     0.69
E H    0.632
G H    0.474
A C    0.672
H H    0.659
D H    0.765
Q H    0.784
V H    0.795
Y H    0.805
E H    0.815
T H    0.807
V H    0.801
R H    0.817
R H    0.813
Y H     0.78
G H    0.765
H H    0.745
E H    0.739
S H     0.73
G H    0.754
E H     0.76
I H    0.745
W H    0.743
H H    0.733
R H    0.728
M H    0.701
Q H    0.683
K H    0.654
N H    0.581
L C    0.494
P C     0.51
G C    0.493
D C    0.467
L H    0.426
A H    0.414
I C    0.388
Q C     0.53
G C    0.621
R C    0.667
END