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Benchmark data sets: 16S

Data sources

  • 16S: The references (structures) and true events (sequences of T) have been extracted from Comparative Rna Web site and project The Gutell Lab
  • noise: sequences of F have been randomly extracted from viral sequences:
    • AF486073.2
    • DQ447655
    • EF452494.1
    • NC_001616.1
    • NC_003839.2

Sets

About the data:

  • size of R (nb of references): 6
  • references length (min/avg/max): 1513 / 1683.33 / 1871
  • size of T: 107
  • size of T2: 2274
  • size of F: 288
  • size of F2: 5752

How to run the benchmarking engine on this benchmark

We assume all requirements are satisfied (see benchmarking tools, and that a file tools.xml is present in the current directory.

mkdir 16S
cd 16S
unzip ../brasero_16S.zip 
cp ../tools.xml .
java -jar ../braseroComparator_1.0.jar -d results references_set true_events_with_viral_noise_set tools.xml
java -jar ../braseroAnalyzer_1.0.jar results
cd results
inkscape -z -A all_snspRoc.pdf all_snspRoc.svg
acroread all_snspRoc.pdf
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Page last modified on December 09, 2010, at 03:22 PM EST