
PFRMAT SS
TARGET T0095
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0095
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-5933/target-align-5933.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 12.0079
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0095
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.alpha.14865/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 Jun  5 21:38:57 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-5933/target-align-5933.a2m
METHOD 
METHOD  guide seq name: T0095
METHOD ###end 0
MODEL 1
D H    0.477
H H     0.48
V H    0.492
S H    0.498
D H    0.619
S H    0.641
F H    0.644
L H    0.607
E H    0.605
T H     0.58
N C    0.456
V H    0.443
P H    0.551
L H    0.672
L H    0.684
V H    0.682
L H    0.679
I H     0.68
E H     0.68
A H    0.665
A H     0.63
K H    0.568
N C    0.548
G C    0.677
N C    0.592
E H    0.661
K H    0.707
E H    0.716
V H    0.743
K H    0.764
E H    0.776
Y H    0.774
A H    0.774
Q H    0.768
V H    0.757
F H    0.767
R H    0.761
E H    0.764
H H    0.745
A H    0.742
N H    0.749
K H    0.746
L H     0.73
I H    0.713
E H     0.71
V H    0.694
A H    0.695
N H    0.674
L H    0.653
A H    0.615
C H    0.508
S C    0.442
I C    0.545
S C    0.637
N C    0.654
N C    0.685
E H    0.569
E H    0.601
G H    0.604
V H    0.681
K H    0.699
L H    0.686
V H    0.687
R H    0.688
M H    0.675
S H    0.674
A H     0.73
S H     0.73
Q H     0.72
L H    0.746
E H    0.744
A H    0.734
L H    0.697
C H    0.653
P H    0.724
Q H    0.751
V H    0.744
I H    0.736
N H    0.734
A H    0.704
A H    0.662
L H    0.639
A H    0.616
L H    0.581
A H    0.497
A C    0.454
K C    0.746
P C    0.664
Q C    0.595
S C    0.493
K H    0.616
L H    0.635
A H    0.664
Q H    0.701
E H    0.716
N H    0.693
M H     0.75
D H    0.766
L H    0.768
F H    0.771
K H    0.778
E H    0.796
Q H    0.783
W H    0.787
E H    0.784
K H    0.783
Q H    0.768
V H    0.789
R H     0.79
V H     0.79
L H     0.79
T H    0.773
D H    0.775
A H    0.759
V H    0.746
D H    0.719
D H    0.693
I H    0.609
T C    0.516
S C    0.587
I H    0.723
D H    0.743
D H    0.754
F H     0.76
L H    0.745
A H    0.707
V H    0.688
S H    0.627
E H    0.802
N H    0.803
H H    0.786
I H    0.769
L H    0.766
E H    0.753
D H    0.713
V H    0.718
N H      0.7
K H    0.707
C H    0.683
V H    0.697
I H     0.69
A H    0.678
L H    0.653
Q H    0.584
E H    0.567
K C     0.53
D C    0.639
V H    0.532
D H    0.541
G H    0.548
L H    0.512
D H    0.495
R H    0.514
T H    0.497
A H    0.577
G H    0.598
A H    0.621
I H    0.571
R H    0.569
G H    0.614
R H    0.642
A H    0.639
A H     0.66
R H    0.656
V H    0.645
I H    0.641
H H     0.63
V H    0.619
V H    0.616
T H    0.616
S H    0.637
E H    0.616
M H    0.551
D H    0.474
N C    0.508
Y C     0.61
E C    0.631
P C     0.63
G C    0.484
V H    0.495
Y H    0.571
T H    0.643
E H    0.735
K H    0.742
V H    0.767
L H    0.779
E H     0.75
A H    0.744
T H    0.728
K H    0.658
L H    0.641
L H    0.558
S H    0.485
N H    0.447
T C    0.499
V C    0.516
M C    0.521
P H    0.464
R H    0.556
F H    0.575
T H    0.534
E H    0.532
Q H    0.583
V H    0.554
E H    0.573
A H    0.599
A H    0.585
V H    0.637
E H    0.638
A H      0.6
L H    0.542
S H    0.458
S C    0.518
D C    0.717
P C    0.702
A C    0.696
Q C    0.691
P C    0.475
M H    0.573
D H    0.603
E H    0.683
N H    0.681
E H    0.673
F H    0.684
I H    0.682
D H    0.668
A H    0.657
S H     0.59
R H    0.635
L H    0.653
V H    0.635
Y H    0.625
D H    0.629
G H    0.635
I H    0.689
R H    0.687
D H    0.689
I H    0.672
R H    0.657
K H    0.659
A H    0.631
V H    0.605
L H    0.459
M C    0.582
END


