Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores

Yang Song, Lei Hua, Bruce A. Shapiro, Jason T.L. Wang

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


RNA pseudoknots play important roles in many biological processes. Previous methods for comparative pseudoknot analysis mainly focus on simultaneous folding and alignment of RNA sequences. Little work has been done to align two known RNA secondary structures with pseudoknots taking into account both sequence and structure information of the two RNAs. Results: In this article we present a novel method for aligning two known RNA secondary structures with pseudoknots. We adopt the partition function methodology to calculate the posterior log-odds scores of the alignments between bases or base pairs of the two RNAs with a dynamic programming algorithm. The posterior log-odds scores are then used to calculate the expected accuracy of an alignment between the RNAs. The goal is to find an optimal alignment with the maximum expected accuracy. We present a heuristic to achieve this goal. The performance of our method is investigated and compared with existing tools for RNA structure alignment. An extension of the method to multiple alignment of pseudoknot structures is also discussed. Conclusions: The method described here has been implemented in a tool named RKalign, which is freely accessible on the Internet.

Original languageEnglish (US)
Article number39
JournalBMC Bioinformatics
Issue number1
StatePublished - Dec 6 2015

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


  • Dynamic programming algorithm
  • RNA secondary structure including pseudoknots
  • Structural alignment


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