Skip to main content
SpringerLink
Log in

Alignment between Two RNA Structures

  • Conference paper
  • First Online:
Mathematical Foundations of Computer Science 2001 (MFCS 2001)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2136))

Abstract

The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the four-letter alphabet {A,C, G, U}. The RNA secondary and tertiary structures can be represented as a set of nested base pairs and a set of crossing base pairs, respectively. These base pairs form bonds between A–U,–C–G, and G–U.

This paper considers alignment with affine gap penalty between two RNA molecule structures. In general this problem is Max SNP-hard for tertiary structures. We present an algorithm for the case where aligned base pairs are non-crossing. Experimental results show that this algorithm can be used for practical application of RNA structure alignment.

Research supported partially by the Natural Sciences and Engineering Research Council of Canada under Grant No. OGP0046373.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. V. Bafna, S. Muthukrishnan, and R. Ravi, ‘Comparing similarity between RNA strings’, Proc. Combinatorial Pattern Matching Conf. 95, LNCS 937, pp. 1–14, 1995

    Google Scholar 

  2. J. W. Brown, ‘The Ribonuclease P Database’, Nucleic Acids Research, 27:314, 1999.

    Article  Google Scholar 

  3. J. H. Chen, S. Y. Le, and J. V. Maizel, ‘Prediction of common secondary structures of RNAs: a genetic algorithm approach’, Nucleic Acids Research, 28:4, pp. 991–999, 2000.

    Article  Google Scholar 

  4. G. Collins, S. Y. Le, and K. Zhang, ‘A new method for computing similarity between RNA structures’, Proceedings of the Second International workshop on Biomolecular Informatics, pp. 761–765, Atlantic City, March 2000.

    Google Scholar 

  5. F. Corpet and B. Michot, ‘RNAlign program: alignment of RNA sequences using both primary and secondary structures’, Comput. Appl. Biosci vol. 10, no. 4, pp. 389–399, 1995.

    Google Scholar 

  6. P. A. Evans, Algorithms and Complexity for Annotated Sequence Analysis, PhD thesis, University of Victoria, 1999.

    Google Scholar 

  7. O. Gotoh, ‘An improved algorithm for matching biological sequences’, J. Mol. Biol., 162, pp. 705–708, 1982.

    Article  Google Scholar 

  8. T. Jiang, G.-H. Lin, B. Ma, and K. Zhang, ‘The longest common subsequence problem for arc-annotated sequences’, Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM 2000), LNCS 1848, pages 154–165, 2000.

    Chapter  Google Scholar 

  9. H. Lenhof, K. Reinert, and M. Vingron. ‘A polyhedral approach to RNA sequence structure alignment’. Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB’98), pages 153–159, 1998.

    Google Scholar 

  10. G.-H. Lin, B. Ma, and K. Zhang, ‘Edit distance between two RNA structures’, to appear Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB’2001), pp. 200–209, 2001.

    Google Scholar 

  11. S. E. Needleman and C. D. Wunsch, ‘A general method applicable to the search for similarities in the amino-acid sequences of two proteins’, J. Mol. Bio., 48, pp. 443–453, 1970

    Article  Google Scholar 

  12. C. H. Papadimitriou and M. Yannakakis, ‘Optimization, approximation, and complexity classes’, J. Comput. System Sciences, vol. 43, pp. 425–440, 1991.

    Article  MATH  MathSciNet  Google Scholar 

  13. Y. Sakakibara, M. Brown, R. Hughey, I. S. Mian, K. Sjölander, R. Underwood, and D. Haussler, ‘Stochastic context-free grammar for tRNA modeling’, Nucleic aids research, vol. 22, no. 23, pp. 5112–5120, 1994.

    Article  Google Scholar 

  14. D. Sankoff, ‘Simultaneous solution of the RNA folding, alignment and protose-quence problems’, SIAM J. Appl. Math vol. 45, no. 5, pp. 810–824, 1985.

    Article  MATH  MathSciNet  Google Scholar 

  15. T. F. Smith and M. S. Waterman, ‘Comparison of biosequences’, Adv. in Appl. Math. 2, pp. 482–489, 1981

    Article  MATH  MathSciNet  Google Scholar 

  16. K. Zhang, L. Wang, and B. Ma, ‘Computing similarity between RNA structures’, Proceedings of the Tenth Symposium on Combinatorial Pattern Matching. LNCS 1645, pp. 281–293, 1999.

    Chapter  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dept. of Computer Science, University of Western Ontario, London, Ont., N6A 5B7, Canada

    Zhuozhi Wang & Kaizhong Zhang

Authors
  1. Zhuozhi Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kaizhong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Mathematical Institute, AS CR, Žitná 25, 115 67, Praha 1, Czech Republic

    Jiří Sgall

  2. Faculty of Mathematics and Physics Institute for Theoretical Computer Science (ITI), Charles University, Malostranské náměstí 25, 118 00, Praha 1, Czech Republic

    Aleš Pultr  & Petr Kolman  & 

Rights and permissions

Reprints and permissions

Copyright information

© 2001 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Wang, Z., Zhang, K. (2001). Alignment between Two RNA Structures. In: Sgall, J., Pultr, A., Kolman, P. (eds) Mathematical Foundations of Computer Science 2001. MFCS 2001. Lecture Notes in Computer Science, vol 2136. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44683-4_60

Download citation

  • DOI: https://doi.org/10.1007/3-540-44683-4_60

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42496-3

  • Online ISBN: 978-3-540-44683-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation