Seed-Based Exclusion Method for Non-coding RNA Gene Search

  • Jean-Eudes Duchesne
  • Mathieu Giraud
  • Nadia El-Mabrouk
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4598)


Given an RNA family characterized by conserved sequences and folding constraints, the problem is to search for all the instances of the RNA family in a genomic database. As seed-based heuristics have been proved very efficient to accelerate the classical homology based search methods such as BLAST, we use a similar idea for RNA structures. We present an exclusion method for RNA search allowing for possible nucleotide insertion, deletion and substitution. It is based on a partition of the RNA stem-loops into consecutive seeds and a preprocessing of the target database. This algorithm can be used to improve time efficiency of current methods, and is guaranteed to find all occurrences that contain at least one exact seed.


Search Phase Position List Target Database Anchor Sequence Canonical Base Pairing 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. Journal of Molecular Biology 215, 403–410 (1990)Google Scholar
  2. 2.
    Bafna, V., Zhang, S.: FastR: Fast database search tool for non-coding RNA. In: Proceedings of IEEE Computational Systems Bioinformatics (CSB) Conference, pp. 52–61 (2004)Google Scholar
  3. 3.
    Eddy, S.R.: RNABOB: a program to search for RNA secondary structure motifs in sequence databases (1992),
  4. 4.
    El-Mabrouk, N., Lisacek, F.: Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome. Journal of Molecular Biology 264, 46–55 (1996)CrossRefGoogle Scholar
  5. 5.
    El-Mabrouk, N., Raffinot, M., Duchesne, J.E., Lajoie, M., Luc, N.: Approximate matching of structured motifs in DNA sequences. J. Bioinformatics and Computational Biology 3(2), 317–342 (2005)CrossRefGoogle Scholar
  6. 6.
    Fichant, G.A., Burks, C.: Identifying potential tRNA genes in genomic DNA sequences. Journal of Molecular Biology 220, 659–671 (1991)CrossRefGoogle Scholar
  7. 7.
    Gautheret, D., Major, F., Cedergren, R.: Pattern searching/alignment with RNA primary and secondary structures. Comput. Appl. Biosci. 6(4), 325–331 (1990)Google Scholar
  8. 8.
    Klein, R., Eddy, S.: RESEARCH: Finding homologs of single structured RNA sequences (2003)Google Scholar
  9. 9.
    Laslett, D., Canback, B.: ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32, 11–16 (2004)CrossRefGoogle Scholar
  10. 10.
    Li, M., Ma, B., Kisman, D., Tromp, J.: PatternHunter II: Highly Sensitive and Fast Homology Search. Journal of Bioinformatics and Computational Biology 2(3), 417–439 (2004) Early version in GIW 2003CrossRefGoogle Scholar
  11. 11.
    Ma, B., Tromp, J., Li, M.: PatternHunter: faster and more sensitive homology search. Bioinformatics 18(3), 440–445 (2002)CrossRefGoogle Scholar
  12. 12.
    Macke, T., Ecker, D., Gutell, R., Gautheret, D., Case, D.A., Sampath, R.: RNAmotif – a new RNA secondary structure definition and discovery algorithm. Nucleic Acids Research 29, 4724–4735 (2001)CrossRefGoogle Scholar
  13. 13.
    Rivas, E., Eddy, S.R.: Secondary Structure Alone is Generally Not Statistically Significant for the Detection of Noncoding RNAs. Bioinformatics 16(7), 583–605 (2000)CrossRefGoogle Scholar
  14. 14.
    Robin, S., Daudin, J.-J., Richard, H., Sagot, M.-F., Schbath, S.: Occurrence probability of structured motifs in random sequences. J. Comp. Biol. 9, 761–773 (2002)CrossRefGoogle Scholar
  15. 15.
    Sagot, M.F., Viari, A.: Flexible identification of structural objects in nucleic acid sequences: palindromes, mirror repeats, pseudoknots and triple helices. In: Hein, J., Apostolico, A. (eds.) Combinatorial Pattern Matching. LNCS, vol. 1264, pp. 224–246. Springer, Heidelberg (1997)Google Scholar
  16. 16.
    Zhang, S., Borovok, I., Aharonovitz, Y., Sharan, R., Bafna, V.: A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. Bioinformatics 22(14), e557–e565 (2006)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Jean-Eudes Duchesne
    • 1
  • Mathieu Giraud
    • 2
  • Nadia El-Mabrouk
    • 1
  1. 1.DIRO – Université de Montréal – H3C 3J7Canada
  2. 2.Bioinfo/Sequoia – LIFL/CNRS, Université de Lille 1France

Personalised recommendations