A comprehensive comparison of comparative RNA structure prediction approaches

BMC Bioinformatics. 2004 Sep 30;5:140. doi: 10.1186/1471-2105-5-140.


Background: An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent benchmarking of these algorithms is rarely performed as is now common practice for protein-folding, gene-finding and multiple-sequence-alignment algorithms.

Results: Here we evaluate a number of RNA folding algorithms using reliable RNA data-sets and compare their relative performance.

Conclusions: We conclude that comparative data can enhance structure prediction but structure-prediction-algorithms vary widely in terms of both sensitivity and selectivity across different lengths and homologies. Furthermore, we outline some directions for future research.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Benchmarking / methods
  • Consensus Sequence / genetics
  • Escherichia coli K12 / genetics
  • Nucleic Acid Conformation*
  • Predictive Value of Tests
  • RNA / genetics*
  • RNA, Bacterial / genetics
  • RNA, Fungal
  • Saccharomyces cerevisiae / genetics
  • Sequence Alignment / methods
  • Software
  • Software Design


  • RNA, Bacterial
  • RNA, Fungal
  • RNA