MultiSETTER - Multiple RNA Structure Similarity Algorithm

  • David Hoksza
  • Peter Szépe
  • Daniel Svozil
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8213)


Recent advances in RNA research and a steady growth of available RNA structures call for bioinformatics methods for handling RNA structural data. Recently, we have introduced SETTER — a fast and accurate method for RNA pairwise structural alignment. In the present contribution we describe its extension for multiple RNA structure alignment called MultiSETTER. It combines SETTER’s decomposition of RNA structures into disjoint fragments with a well known multiple sequence alignment algorithm ClustalW adapted for the structural alignment. We demonstrate the validity of our approach on the task of automatic classification of RNA structures.


structural bioinformatics RNA tertiary structure structural similarity 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Eddy, S.R.: Non coding RNA genes and the modern RNA world. Nature Reviews Genetics 2(12), 919–929 (2001)CrossRefGoogle Scholar
  2. 2.
    Bartel, D.P.: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004)CrossRefGoogle Scholar
  3. 3.
    Hoksza, D., Svozil, D.: Efficient RNA pairwise structure comparison by setter method. Bioinformatics 28(14), 1858–1864 (2012)CrossRefGoogle Scholar
  4. 4.
    Cech, P., Svozil, D., Hoksza, D.: Setter: web server for RNA structure comparison. Nucleic Acids Research 40(Web-Server-Issue), 42–48 (2012)CrossRefGoogle Scholar
  5. 5.
    Kiryu, H., Tabei, Y., Kin, T., Asai, K.: Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics 23(13), 1588–1598 (2007)CrossRefGoogle Scholar
  6. 6.
    Moretti, S., Wilm, A., Higgins, D.G., Xenarios, I., Notredame, C.: R-coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Research 36(Web-Server-Issue), 10–13 (2008)CrossRefGoogle Scholar
  7. 7.
    Katoh, K., Misawa, K., Kuma, K.I., Miyata, T.: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30(14), 3059–3066 (2002)CrossRefGoogle Scholar
  8. 8.
    Torarinsson, E., Havgaard, J.H., Gorodkin, J.: Multiple structural alignment and clustering of RNA sequences. Bioinformatics 23(8), 926–932 (2007)CrossRefGoogle Scholar
  9. 9.
    Tabei, Y., Kiryu, H., Kin, T., Asai, K.: A fast structural multiple alignment method for long RNA sequences. BMC Bioinformatics 9(1), 33 (2008)Google Scholar
  10. 10.
    Chang, Y.F., Huang, Y.L., Lu, C.L.: Sarsa: a web tool for structural alignment of RNA using a structural alphabet. Nucleic Acids Res. 36, 19–24 (2008)CrossRefGoogle Scholar
  11. 11.
    Hendrix, D.K., Brenner, S.E., Holbrook, S.R.: RNA structural motifs: building blocks of a modular biomolecule. Quarterly Reviews of Biophysics 38(3), 221–243 (2005)CrossRefGoogle Scholar
  12. 12.
    Holbrook, S.R.: Structural principles from large RNAs. Annual Review of Biophysics 37(1), 445–464 (2008)MathSciNetCrossRefGoogle Scholar
  13. 13.
    Kabsch, W.: A solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A 32(5), 922–923 (1976)CrossRefGoogle Scholar
  14. 14.
    Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., Mcwilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., Higgins, D.G.: ClustalW and ClustalX version 2.0. Bioinformatics 23, 2947–2948 (2007)CrossRefGoogle Scholar
  15. 15.
    Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4), 406–425 (1987)Google Scholar
  16. 16.
    Klosterman, P.S., Tamura, M., Holbrook, S.R., Brenner, S.E.: SCOR: a Structural Classification of RNA database. Nucleic Acids Res. 30(1), 392–394 (2002)CrossRefGoogle Scholar
  17. 17.
    Tamura, M., Hendrix, D.K., Klosterman, P.S., Schimmelman, N.R., Brenner, S.E., Holbrook, S.R.: SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res. 32(Database issue) (January 2004)Google Scholar

Copyright information

© Springer International Publishing Switzerland 2013

Authors and Affiliations

  • David Hoksza
    • 1
  • Peter Szépe
    • 1
  • Daniel Svozil
    • 2
  1. 1.FMP, Department of Software EngineeringCharles University in PraguePragueCzech Republic
  2. 2.Laboratory of Informatics and ChemistryInstitute of Chemical TechnologyPragueCzech Republic

Personalised recommendations