
PFRMAT SS
TARGET T0126
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0126
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-8682/target-align-8682.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 2.65199
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0126
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.26040/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: Wed Aug 23 11:36:09 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-8682/target-align-8682.a2m
METHOD 
METHOD  guide seq name: T0126
METHOD ###end 0
MODEL 1
M C    0.697
A C    0.652
E C    0.664
D C    0.694
G C    0.758
P C    0.711
Q C    0.633
K C    0.584
Q C    0.524
Q C    0.436
L C     0.43
E C    0.469
M C    0.548
P C    0.549
L E    0.387
V E     0.38
L C    0.463
D C    0.547
Q C    0.511
D C    0.501
L H    0.442
T H    0.454
Q H    0.544
Q H    0.539
M H    0.542
R H    0.534
L H    0.519
R H    0.541
V H      0.6
E H    0.612
S H    0.632
L H    0.669
K H    0.659
Q H    0.631
R H    0.517
G C    0.606
E C    0.635
K C    0.599
K C    0.557
Q C    0.546
D C     0.59
G C    0.492
E H    0.449
K H    0.457
L H    0.419
I H    0.352
R C    0.522
P C    0.541
A C    0.528
E C    0.475
S C     0.36
V E    0.473
Y E    0.507
R E    0.501
L E    0.462
D C    0.416
F C    0.408
I C    0.464
Q H    0.511
Q H    0.513
Q H    0.492
K H    0.427
L E    0.366
Q E    0.411
F E    0.438
D E    0.451
H E    0.503
W E    0.575
N E    0.614
V E     0.65
V E    0.649
L E    0.608
D C    0.501
K C    0.694
P C    0.753
G C    0.648
K E    0.482
V E    0.728
T E    0.738
I E    0.688
T E    0.502
G C    0.572
T C    0.628
S C    0.594
Q C    0.593
N C    0.592
W C    0.567
T C    0.615
P C     0.54
D C     0.52
L H    0.559
T H     0.55
N H      0.6
L H    0.628
M H    0.589
T H    0.584
R H    0.661
Q H    0.606
L H    0.557
L C    0.502
D C    0.702
P C    0.577
A C     0.45
A E    0.378
I E    0.504
F E    0.531
W E    0.473
R C    0.427
K C    0.554
E C    0.651
D C    0.625
S C    0.603
D C    0.576
A C    0.455
M C     0.44
D C    0.485
W H    0.471
N C    0.471
E H    0.654
A H    0.638
D H    0.632
A H     0.77
L H     0.77
E H    0.767
F H    0.739
G H    0.677
E H    0.701
R H    0.704
L H    0.739
S H    0.716
D H    0.724
L H    0.778
A H    0.754
K H    0.739
I H    0.703
R H    0.653
K H     0.63
V H    0.597
M H    0.547
Y H    0.483
F E    0.454
L E    0.596
I E     0.61
T E    0.556
F E    0.401
G C    0.568
E C    0.646
G C    0.713
V C    0.693
E C     0.74
P C    0.621
A C    0.531
N C    0.427
L E    0.371
K E    0.434
A E    0.466
S E    0.507
V E    0.527
V E    0.486
F E    0.393
N C    0.467
Q C    0.564
L C    0.682
END


