
PFRMAT SS
TARGET T0091
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0091
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-22140/target-align-22140.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 22.6041
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0091
METHOD  model_file: ./tmp.alpha.12439/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 12:13:35 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-22140/target-align-22140.a2m
METHOD 
METHOD  guide seq name: T0091
METHOD ###end 0
MODEL 1
M C    0.649
F C    0.653
G C    0.664
K C     0.63
G C    0.622
G C    0.635
L H    0.698
G H    0.742
G H    0.737
L H    0.774
M H    0.819
K H    0.843
Q H    0.845
A H    0.852
Q H     0.86
Q H    0.849
M H    0.838
Q H    0.864
E H    0.874
K H    0.854
M H    0.854
Q H    0.852
K H    0.839
M H    0.831
Q H    0.842
E H    0.846
E H    0.818
I H    0.774
A H    0.685
Q H    0.585
L H    0.429
E E    0.348
V E    0.417
T E    0.419
G E    0.408
E C    0.444
S C    0.592
G C    0.665
A C    0.643
G C    0.471
L E    0.613
V E    0.715
K E    0.744
I E    0.756
T E    0.722
I E    0.656
N E    0.453
G C    0.605
A C    0.615
H C    0.483
N E     0.45
C E    0.546
R E    0.555
R E     0.57
I E    0.563
D E    0.542
I E    0.419
D C    0.647
P H    0.567
S H    0.613
L H     0.61
M H    0.585
E H    0.572
D H    0.581
D H    0.528
K H    0.806
E H     0.85
M H    0.852
L H    0.876
E H    0.892
D H    0.898
L H    0.887
I H    0.876
A H    0.879
A H    0.875
A H    0.862
F H    0.853
N H    0.863
D H    0.869
A H    0.844
V H    0.835
R H    0.829
R H     0.81
A H    0.812
E H    0.825
E H    0.836
L H    0.812
Q H    0.806
K H     0.82
E H    0.822
K H    0.801
M H    0.789
A H    0.757
S H    0.758
V H    0.724
T H    0.674
A H    0.607
G H    0.547
M C    0.529
P C    0.759
L C    0.796
P C    0.816
P C    0.731
G C    0.699
M C    0.695
K C    0.688
F C    0.654
P C    0.618
F C    0.652
END


