CentroidAlign-Web: A fast and accurate multiple aligner for long non-coding RNAs

Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada*

*Corresponding author for this work

Research output: Contribution to journalLetterpeer-review

3 Citations (Scopus)


Due to the recent discovery of non-coding RNAs (ncRNAs), multiple sequence alignment (MSA) of those long RNA sequences is becoming increasingly important for classifying and determining the functional motifs in RNAs. However, not only primary (nucleotide) sequences, but also secondary structures of ncRNAs are closely related to their function and are conserved evolutionarily. Hence, information about secondary structures should be considered in the sequence alignment of ncRNAs. Yet, in general, a huge computational time is required in order to compute MSAs, taking secondary structure information into account. In this paper, we describe a fast and accurate web server, called CentroidAlign-Web, which can handle long RNA sequences. The web server also appropriately incorporates information about known secondary structures into MSAs. Computational experiments indicate that our web server is fast and accurate enough to handle long RNA sequences. CentroidAlign-Web is freely available from http://centroidalign.ncrna.org/.

Original languageEnglish
Pages (from-to)6144-6156
Number of pages13
JournalInternational journal of molecular sciences
Issue number3
Publication statusPublished - 2013 Mar
Externally publishedYes


  • Consensus structures
  • Multiple sequence alignment (MSA)
  • NcRNAs
  • RRNAs
  • Secondary structure
  • Structural alignment
  • Web server

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry


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