
PFRMAT SS
TARGET T0112
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0112
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-21144/target-align-21144.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 470.861
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0112
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.32313/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 15:45:01 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-21144/target-align-21144.a2m
METHOD 
METHOD  guide seq name: T0112
METHOD ###end 0
MODEL 1
M C    0.654
A H    0.572
S H    0.599
D H    0.595
N H    0.587
L H    0.585
S H    0.576
A H    0.536
V H    0.477
L H    0.375
Y C    0.556
K C    0.695
Q C    0.695
N C    0.649
D C    0.493
L E    0.526
R E    0.584
L E    0.586
E E    0.559
Q E    0.507
R E    0.429
P C     0.52
I C      0.6
P C    0.659
E C    0.677
P C    0.694
K C    0.743
E C    0.703
D C    0.631
E E    0.396
V E    0.622
L E    0.677
L E     0.69
Q E    0.666
M E    0.665
A E    0.633
Y E    0.606
V E    0.559
G E    0.495
I C    0.452
C C    0.594
G C     0.45
S H    0.429
D H     0.48
V H    0.503
H H    0.483
Y H    0.477
Y H     0.45
E H    0.378
H C    0.533
G C    0.592
R C      0.6
I C     0.62
A C    0.629
D C    0.651
F C    0.586
I C    0.495
V C    0.498
K C    0.586
D C     0.63
P C    0.619
M C    0.494
V C     0.44
I C    0.499
G C    0.611
H C    0.511
E C    0.428
A E     0.43
S E    0.479
G E    0.525
T E    0.612
V E    0.674
V E    0.637
K E    0.582
V E    0.456
G C    0.648
K C    0.669
N C     0.63
V C    0.546
K C    0.519
H C    0.457
L C    0.467
K C    0.551
K C    0.559
G C    0.667
D C    0.633
R E    0.526
V E    0.667
A E    0.676
V E    0.621
E E    0.513
P C    0.433
G C    0.498
V C    0.549
P C    0.587
C C     0.62
R C    0.609
R C    0.568
C C    0.615
Q C    0.516
F C    0.457
C C    0.449
K C    0.456
E C    0.525
G C    0.606
K C    0.539
Y C    0.501
N C    0.488
L C    0.476
C C    0.576
P C    0.594
D C    0.635
L C     0.59
T C    0.515
F C     0.43
C E    0.419
A C    0.454
T C    0.505
P C    0.541
P C    0.554
D C     0.62
D C    0.608
G C    0.604
N C    0.503
L C    0.376
A E    0.425
R E    0.475
Y E    0.542
Y E    0.585
V E    0.575
H E    0.486
A C    0.493
A C    0.454
D C    0.446
F C    0.392
C E    0.422
H E    0.455
K E    0.413
L C    0.572
P C    0.716
D C     0.69
N C    0.685
V C    0.667
S C     0.68
L H    0.574
E H    0.591
E H    0.612
G H    0.533
A H    0.499
L H    0.452
L C    0.416
E C     0.49
P H    0.485
L H    0.537
S H     0.55
V H    0.573
G H    0.603
V H    0.619
H H    0.623
A H    0.622
C H    0.612
R H    0.595
R H    0.569
A C    0.443
G C    0.644
V C    0.609
Q C    0.669
L C    0.685
G C    0.687
T C    0.598
T E    0.568
V E    0.716
L E    0.736
V E    0.732
I E     0.64
G C    0.497
A C    0.624
G C    0.624
P H    0.591
I H    0.646
G H    0.673
L H    0.703
V H    0.722
S H    0.741
V H    0.759
L H    0.758
A H    0.762
A H    0.768
K H    0.758
A H    0.734
Y H    0.633
G C    0.648
A C    0.684
F E    0.505
V E    0.696
V E    0.711
C E    0.669
T E    0.565
A C    0.501
R C    0.638
S C    0.689
P H    0.631
R H    0.667
R H    0.694
L H    0.754
E H    0.768
V H    0.775
A H    0.775
K H    0.771
N H    0.757
C H    0.619
G C    0.691
A C    0.709
D C    0.548
V E    0.501
T E    0.591
L E    0.546
V C    0.467
V C    0.563
D C    0.609
P C    0.591
A C    0.584
K C    0.572
E C    0.459
E H    0.441
E H    0.619
S H    0.503
S H    0.617
I H     0.72
I H    0.748
E H    0.762
R H    0.754
I H    0.755
R H    0.741
S H    0.718
A H    0.685
I H    0.591
G C    0.485
D C    0.571
L C    0.718
P C    0.613
N C    0.519
V E    0.613
T E    0.647
I E    0.633
D E    0.544
C C    0.426
S C    0.512
G C    0.593
N C    0.509
E H    0.505
K H    0.572
C H    0.595
I H    0.654
T H    0.678
I H    0.693
G H    0.691
I H    0.696
N H    0.686
I H    0.663
T H    0.611
R C    0.437
T C    0.523
G C     0.65
G C    0.631
T E    0.491
L E    0.676
M E    0.709
L E    0.695
V E    0.624
G E    0.437
M C    0.544
G C    0.622
S C    0.664
Q C    0.634
M C    0.584
V C    0.538
T C     0.53
V C    0.506
P C    0.548
L H    0.441
V H    0.471
N H    0.507
A H    0.472
C H    0.417
A H    0.391
R C    0.393
E C    0.417
I E    0.381
D E    0.502
I E    0.551
K E    0.527
S E    0.479
V E    0.401
F C    0.437
R C    0.523
Y C    0.572
C C    0.499
N H    0.446
D H    0.517
Y H    0.704
P H    0.744
I H    0.754
A H    0.755
L H    0.754
E H    0.752
M H    0.743
V H    0.726
A H    0.697
S H    0.636
G C    0.611
R C    0.579
C C    0.549
N C    0.579
V C    0.498
K C    0.538
Q C    0.475
L C    0.413
V C    0.353
T C    0.404
H C    0.405
S C    0.396
F C    0.496
K C    0.615
L H    0.648
E H    0.683
Q H    0.715
T H    0.762
V H    0.787
D H    0.802
A H    0.798
F H    0.795
E H    0.789
A H     0.78
A H    0.757
R H    0.715
K H    0.621
K C    0.612
A C    0.781
D C    0.485
N E    0.374
T E    0.481
I E    0.559
K E    0.629
V E    0.679
M E    0.668
I E    0.565
S C    0.631
C C    0.855
R C    0.843
Q C    0.834
G C    0.862
END


