
PFRMAT SS
TARGET T0110
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0110
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-2191/target-align-2191.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 21.99
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0110
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.7343/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: Mon Jul 10 13:02:06 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-2191/target-align-2191.a2m
METHOD 
METHOD  guide seq name: T0110
METHOD ###end 0
MODEL 1
M C    0.559
A C    0.611
R C    0.583
E C     0.49
F H    0.568
K H    0.631
R H    0.651
S H    0.735
D H    0.765
R H    0.771
V H     0.77
A H    0.799
Q H    0.836
E H    0.834
I H    0.838
Q H     0.85
K H    0.863
E H    0.849
I H    0.833
A H    0.821
V H    0.818
I H    0.796
L H    0.773
Q H    0.732
R H    0.678
E H    0.599
V H    0.444
K C    0.561
D C    0.706
P C    0.617
R C    0.526
I C    0.509
G C    0.525
M E    0.454
V E    0.591
T E    0.641
V E     0.64
S E     0.55
D E    0.566
V E     0.61
E E    0.607
V E    0.572
S C    0.426
S C    0.573
D C    0.595
L C    0.424
S E    0.373
Y E    0.521
A E    0.558
K E    0.628
I E    0.694
F E     0.71
V E     0.69
T E    0.642
F E    0.517
L C    0.499
F C    0.642
D C    0.674
H C    0.659
D C    0.715
E H    0.516
M H    0.583
A H     0.61
I H    0.708
E H    0.751
Q H    0.756
G H    0.758
M H    0.781
K H    0.786
G H    0.778
L H     0.78
E H    0.769
K H    0.765
A H    0.745
S H    0.737
P H    0.682
Y H    0.703
I H    0.715
R H    0.735
S H    0.741
L H    0.736
L H    0.724
G H    0.698
K H    0.687
A H    0.604
M H    0.487
R C    0.371
L E    0.368
R E    0.422
I E    0.418
V C    0.552
P C    0.548
E E    0.387
I E    0.507
R E    0.554
F E    0.598
I E    0.542
Y E    0.403
D C    0.498
Q C    0.495
S C    0.453
L H    0.471
V H    0.479
E H    0.541
G H    0.628
M H    0.657
R H    0.673
M H    0.745
S H    0.757
N H    0.776
L H    0.765
V H    0.757
T H    0.733
N H    0.709
V H    0.663
V H    0.609
R H    0.631
E H    0.562
D H    0.533
E H    0.528
K H    0.506
K H     0.43
H C    0.399
V C    0.449
E C     0.58
E C    0.629
S C    0.683
N C    0.745
END


