
PFRMAT SS
TARGET T0093
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0093
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-31977/target-align-31977.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 47.5325
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0093
METHOD  model_file: ./tmp.alpha.17499/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 May 20 12:28:28 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-31977/target-align-31977.a2m
METHOD 
METHOD  guide seq name: T0093
METHOD ###end 0
MODEL 1
M C    0.607
L E    0.525
D E    0.637
I E    0.688
V E    0.689
L E    0.632
Y E    0.498
E C    0.558
P C    0.632
E C    0.657
I C    0.758
P C    0.703
Q C    0.651
N C    0.638
T H    0.591
G H    0.617
N H    0.639
I H     0.67
I H    0.683
R H    0.698
L H    0.705
C H    0.707
A H    0.696
N H    0.672
T H    0.554
G C     0.64
F C    0.649
R E    0.481
L E    0.614
H E    0.658
L E     0.67
I E      0.6
E C    0.458
P C    0.584
L C     0.55
G C    0.502
F C    0.478
T C    0.473
W C     0.48
D C    0.515
D C    0.512
K H    0.643
R H    0.639
L H    0.644
R H    0.635
R H    0.642
S H    0.603
G H    0.528
L C    0.468
D C    0.501
Y H    0.459
H H    0.442
E H    0.434
F H    0.358
A C     0.38
E C    0.419
I E     0.48
K E    0.499
R E    0.474
H E    0.386
K C    0.458
T C    0.558
F H    0.724
E H    0.752
A H    0.763
F H    0.752
L H    0.754
E H     0.72
S H    0.683
E H    0.592
K H     0.51
P H    0.478
K C    0.584
R C    0.639
L E    0.433
F E    0.622
A E    0.672
L E    0.653
T E    0.553
T C    0.449
K C    0.628
G C    0.646
C C    0.594
P C    0.542
A C    0.538
H H    0.466
S H    0.479
Q H    0.484
V C      0.4
K C    0.486
F C    0.561
K C    0.625
L C    0.631
G C    0.585
D E    0.502
Y E    0.631
L E    0.691
M E    0.688
F E    0.629
G C     0.48
P C    0.601
E C    0.549
T C    0.482
R C    0.573
G C    0.717
I C    0.702
P C    0.662
M H    0.635
S H    0.658
I H    0.658
L H    0.647
N H    0.628
E H      0.6
M C    0.547
P C    0.624
M C    0.577
E C    0.597
Q C    0.455
K E    0.529
I E    0.612
R E    0.606
I E     0.49
P C    0.529
M C    0.577
T C    0.606
A C    0.573
N C    0.544
S C    0.494
R H    0.435
S H    0.514
M H    0.566
N H    0.572
L H    0.631
S H    0.657
N H      0.7
S H    0.712
V H    0.712
A H    0.713
V H    0.701
T H    0.699
V H    0.712
Y H    0.744
E H    0.748
A H    0.751
W H    0.735
R H    0.731
Q H    0.695
L H    0.617
G H    0.505
Y H    0.454
K C    0.455
G C    0.533
A C    0.493
V C    0.462
N C    0.483
L C    0.606
P C    0.643
E C    0.646
V C    0.657
K C    0.696
END


