Locality and gaps in RNA comparison

Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M. Landau, Mikhail A. Roytberg, Oren Weimann, Kaizhong Zhang

Research output: Contribution to journalArticlepeer-review


Locality is an important and well-studied notion in comparative analysis of biological sequences. Similarly, taking into account affine gap penalties when calculating biological sequence alignments is a well-accepted technique for obtaining better alignments. When dealing with RNA, one has to take into consideration not only sequential features, but also structural features of the inspected molecule. This makes the computation more challenging, and usually prohibits the comparison only to small RNAs. In this paper we introduce two local metrics for comparing RNAs that extend the Smith-Waterman metric and its normalized version used for string comparison. We also present a global RNA alignment algorithm which handles affine gap penalties. Our global algorithm runs in O(m2n(1 + lg n/m)) time, while our local algorithms run in O(m2n(1 + lg n/m)) and O(n2m) time, respectively, where m ≤ n are the lengths of the two given RNAs. These time complexities are comparable to the time complexity of any known RNA alignment algorithm. Furthermore, both our global and local algorithms are robust to selections of arbitrary scoring schemes.

Original languageEnglish
Pages (from-to)1074-1087
Number of pages14
JournalJournal of Computational Biology
Issue number8
StatePublished - 1 Oct 2007


  • Affine gap penalties
  • Alignment
  • Gaps
  • Local alignment
  • Pairwise comparison
  • RNA

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


Dive into the research topics of 'Locality and gaps in RNA comparison'. Together they form a unique fingerprint.

Cite this