
PFRMAT SS
TARGET T0105
AUTHOR 2000-8506-6614
METHOD This prediction was derived from the following methods
METHOD by averaging the corresponding probabilities: 
METHOD Method 0:
METHOD  TARGET T0105
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-10803/target-align-10803.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 13.7462
METHOD 
METHOD  CHAIN 1
METHOD Method 1:
METHOD  Prediction using SAM HMM nearest-neighbor
METHOD  sequence: T0105
METHOD  model_file: /projects/compbio/tmp/sam-nn-tmp.beta.26928/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: Thu Jul  6 00:40:14 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-10803/target-align-10803.a2m
METHOD 
METHOD  guide seq name: T0105
METHOD ###end 0
MODEL 1
D C    0.657
E C    0.636
N C    0.659
I C    0.546
N C    0.532
F C    0.462
K C    0.514
Q C    0.547
S C    0.578
E C    0.543
L C    0.534
P C    0.575
V E    0.457
T E    0.423
C C    0.516
G C    0.549
E C    0.503
V E    0.384
K E    0.441
G E     0.48
T E    0.545
L E     0.58
Y E    0.551
K E    0.513
E E    0.466
R E     0.46
F C    0.392
K C    0.592
Q C     0.65
G C    0.699
T C    0.658
S C    0.564
K E    0.422
K E    0.517
C E    0.631
I E    0.647
Q E    0.593
S E    0.465
E C    0.617
D C    0.678
K C    0.657
K C    0.494
W E    0.517
F E    0.462
T C    0.639
P C     0.67
R C    0.597
E E    0.384
F E    0.486
E E    0.498
I E     0.45
E C    0.474
G C    0.618
D C    0.686
R C    0.635
G C    0.562
A C    0.544
S C    0.502
K H    0.499
N H    0.521
W H    0.632
K H    0.645
L H    0.647
S H    0.615
I H    0.615
R H    0.603
C H    0.553
G C    0.461
G C    0.615
Y C    0.548
T C    0.466
L H    0.632
K H    0.653
V H    0.665
L H    0.666
M H    0.657
E H    0.646
N H    0.612
K C    0.555
F C    0.559
L C    0.576
P C    0.634
E C    0.622
P C    0.612
P C    0.579
S C    0.646
T C    0.611
R C    0.549
K C    0.495
K C    0.504
V C    0.582
T C    0.625
I C    0.661
K C    0.808
END


