
PFRMAT SS
TARGET T0113
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0113
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-22500/target-align-22500.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 673.21
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0113
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.7403/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: Thu Jul 13 15:42:09 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-22500/target-align-22500.a2m
METHOD 
METHOD  guide seq name: T0113
METHOD ###end 0
MODEL 1
M C    0.576
A C    0.508
A C    0.466
A C    0.453
V C    0.472
R C    0.496
S C    0.552
V C    0.604
K C    0.658
G C     0.68
L C    0.602
V E    0.659
A E    0.764
V E    0.793
I E    0.764
T E    0.608
G C    0.595
G C    0.702
A C    0.598
S C    0.482
G H    0.505
L H    0.586
G H    0.638
L H    0.727
S H    0.744
T H    0.764
A H     0.79
K H    0.802
R H    0.797
L H    0.792
V H    0.775
G H    0.754
Q H    0.611
G C    0.665
A C    0.678
T E    0.499
A E    0.713
V E    0.721
L E    0.687
L E    0.604
D C     0.42
V C    0.595
P C    0.675
N H    0.558
S H    0.672
E H     0.72
G H    0.753
E H    0.774
T H     0.78
E H    0.776
A H    0.778
K H    0.769
K H    0.746
L H    0.612
G C    0.651
G C    0.661
N C    0.527
C E     0.48
I E     0.59
F E     0.62
A E    0.603
P E    0.563
A E     0.44
N C    0.535
V C    0.549
T C    0.621
S C    0.684
E H    0.689
K H    0.736
E H    0.743
V H    0.787
Q H    0.802
A H     0.81
A H    0.802
L H    0.806
T H    0.805
L H    0.793
A H    0.777
K H    0.773
E H    0.759
K H    0.723
F H    0.593
G C    0.625
R C    0.632
I C    0.489
D E     0.38
V E    0.621
A E    0.647
V E    0.626
N E    0.502
C C    0.498
A C    0.484
G C    0.478
I C    0.463
A C    0.498
V C    0.546
A C    0.563
I C    0.577
K C    0.521
T C    0.488
Y C    0.484
H C    0.556
E C    0.575
K C    0.575
K C    0.565
N C    0.494
Q C    0.496
V C    0.527
H C    0.592
T C    0.666
L H    0.644
E H    0.665
D H    0.659
F H    0.665
Q H    0.669
R H    0.666
V H     0.65
I H    0.624
N H    0.574
V H    0.532
N H    0.438
L H    0.526
I H    0.602
G H    0.617
T H    0.645
F H     0.66
N H    0.666
V H     0.67
I H    0.686
R H    0.714
L H    0.705
V H    0.688
A H    0.658
G H    0.639
V H    0.619
M H    0.596
G H    0.561
Q H    0.538
N C    0.507
E C    0.555
P C    0.546
D C    0.575
Q C    0.628
G C    0.693
G C    0.705
Q C    0.665
R C    0.619
G C    0.467
V E    0.611
I E    0.724
I E    0.732
N E    0.688
T E    0.618
A E    0.442
S C     0.44
V C    0.396
A C    0.391
A C    0.408
F C    0.427
E C    0.475
G C    0.563
Q C    0.599
V C    0.571
G C    0.521
Q C    0.462
A H    0.444
A H    0.541
Y H    0.573
S H    0.607
A H    0.645
S H    0.667
K H    0.716
G H    0.699
G H    0.691
I H      0.7
V H    0.702
G H    0.704
M H    0.702
T H    0.704
L H    0.727
P H    0.719
I H    0.716
A H    0.716
R H    0.707
D H    0.689
L H    0.645
A H      0.5
P H    0.462
I C    0.521
G C    0.659
I C    0.532
R E    0.616
V E    0.684
V E    0.664
T E     0.66
I E    0.611
A C    0.498
P C    0.615
G C    0.645
L C    0.548
F C    0.509
A C    0.549
T C    0.566
P C    0.509
L C    0.433
L C    0.412
T H     0.42
T C    0.456
L C    0.453
P C    0.501
D H    0.563
K H    0.617
V H    0.652
R H    0.656
N H    0.671
F H    0.673
L H    0.653
A H    0.634
S H    0.593
Q H    0.535
V H    0.443
P C    0.497
F C    0.521
P C     0.52
S C    0.565
R C    0.551
L C    0.591
G C    0.631
D C    0.717
P H    0.614
A H    0.679
E H    0.691
Y H    0.704
A H    0.705
H H    0.707
L H    0.692
V H    0.681
Q H    0.675
M H    0.664
V H    0.645
I H     0.57
E C    0.442
N C    0.561
P C    0.596
F C    0.531
L C    0.541
N C    0.525
G C    0.462
E E    0.466
V E    0.625
I E    0.661
R E    0.627
L E     0.52
D C    0.582
G C    0.662
A C    0.685
I C    0.533
R C    0.496
M C     0.56
Q C    0.693
P C    0.815
END


