PFRMAT SS
TARGET T0124
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0124
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-29043/target-align-29043.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 20.7233
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0124
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.32592/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: Tue Aug 22 12:48:42 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-29043/target-align-29043.a2m
METHOD 
METHOD  guide seq name: T0124
METHOD ###end 0
MODEL 1
N C    0.678
M C    0.521
K C    0.434
E H    0.424
V H    0.458
T H    0.407
Q H    0.423
L C    0.477
P C    0.466
E C    0.462
P C     0.48
Q C    0.547
T C    0.571
A C    0.565
S C    0.586
L H     0.73
A H    0.758
E H    0.768
L H    0.772
Q H    0.758
Q H    0.728
M H    0.761
K H    0.781
L H    0.771
F H    0.798
L H    0.802
K H    0.812
L H    0.796
L H    0.774
K H    0.779
K H    0.787
Q H    0.767
E H    0.803
K H    0.839
E H    0.833
L H    0.853
K H    0.855
E H    0.862
L H    0.848
E H    0.836
R H    0.834
K H    0.802
G H    0.686
S H    0.732
K H    0.758
R H    0.737
R H    0.744
E H    0.732
E H    0.738
L H    0.754
L H    0.745
Q H    0.737
K H    0.693
Y H    0.626
S H     0.55
V H    0.519
L H    0.467
F H    0.452
L C    0.444
E C    0.465
P C    0.505
V C    0.522
Y C    0.578
P C    0.593
R C     0.58
G C    0.612
L C    0.625
D C    0.635
S C    0.575
Q H    0.486
V H    0.552
V H     0.65
E H    0.694
L H    0.734
K H    0.756
E H    0.785
R H    0.811
L H    0.802
E H    0.811
M H    0.831
E H     0.83
L H    0.833
I H    0.831
H H     0.83
L H    0.814
G H    0.802
E H    0.812
E H    0.815
Y H    0.778
H H    0.763
D H    0.782
G H    0.795
I H    0.802
R H    0.806
R H    0.802
R H    0.799
K H    0.795
E H    0.816
Q H    0.816
H H    0.804
A H    0.807
T H    0.832
E H    0.845
Q H    0.842
T H    0.849
A H    0.861
K H    0.862
I H     0.86
T H    0.858
E H    0.855
L H    0.841
A H     0.83
R H    0.817
E H    0.796
K H    0.773
Q H    0.766
I H     0.78
A H    0.777
E H    0.789
L H    0.821
K H    0.845
A H    0.841
L H    0.831
K H    0.813
E H    0.799
S H    0.739
S H    0.609
E H    0.763
S H    0.753
N H    0.721
I H    0.781
K H    0.805
D H    0.818
I H    0.837
K H    0.829
K H    0.843
K H    0.814
L H    0.796
E H    0.747
A H    0.743
K H    0.671
R H    0.597
L H    0.693
D H    0.671
R H    0.668
I H    0.731
Q H     0.73
V H    0.728
M H    0.671
M H    0.558
R H    0.585
S H    0.529
T H    0.468
S H    0.462
D C    0.495
K H    0.677
A H    0.694
A H    0.723
Q H     0.72
E H    0.735
R H    0.747
L H    0.729
K H    0.756
K H    0.748
E H    0.742
I H    0.744
N H    0.669
N H    0.703
S H    0.681
H H    0.691
I H    0.752
Q H     0.78
E H    0.791
V H    0.776
V H      0.8
Q H    0.813
T H    0.816
I H    0.834
K H    0.834
L H     0.83
L H    0.822
T H    0.807
E H    0.798
K H    0.772
T H    0.728
A H    0.646
R H    0.708
Y H    0.795
Q H    0.838
Q H    0.879
K H    0.878
L H    0.871
E H    0.856
E H    0.867
K H    0.856
Q H    0.846
A H    0.853
E H    0.863
N H    0.856
L H    0.857
R H    0.863
A H    0.856
I H    0.846
Q H    0.835
E H    0.825
K H    0.777
E H    0.724
G H    0.758
Q H    0.788
L H     0.81
Q H    0.846
Q H    0.854
E H    0.839
A H    0.821
V H    0.811
A H    0.818
E H     0.79
Y H    0.778
E H    0.766
E H    0.756
K H    0.704
L H    0.663
K H      0.6
T H    0.536
L H     0.45
T C    0.454
V H    0.471
E H    0.486
V H    0.509
Q H     0.53
E H     0.58
M H    0.581
V H    0.573
K H    0.583
N H    0.533
Y H    0.453
M C    0.512
K C    0.469
E C    0.497
V C    0.526
F C    0.597
P C    0.679
END