How to benchmark RNA secondary structure prediction accuracy

Methods. 2019 Jun 1:162-163:60-67. doi: 10.1016/j.ymeth.2019.04.003. Epub 2019 Apr 2.


RNA secondary structure prediction is widely used. As new methods are developed, these are often benchmarked for accuracy against existing methods. This review discusses good practices for performing these benchmarks, including the choice of benchmarking structures, metrics to quantify accuracy, the importance of allowing flexibility for pairs in the accepted structure, and the importance of statistical testing for significance.

Keywords: Comparative sequence analysis; RNA folding.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Computational Biology / standards
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA / genetics
  • Sequence Analysis, RNA / methods*
  • Sequence Analysis, RNA / standards
  • Software


  • RNA