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Advances in Bioinformatics
Volume 2012, Article ID 893048, 5 pages
http://dx.doi.org/10.1155/2012/893048
Resource Review

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

1LaBRI, UMR 5800 CNRS, Université Bordeaux, 351, Cours de la Libération, 33405 Talence Cédex, France
2The Pacific Institute for the Mathematical Sciences, University of British Columbia, CNRS UMI 3069, 200-1933 West Mall Vancouver, BC, Canada V6T 1Z2
3LRI, UMR 8623 CNRS, Université Paris-Sud and INRIA Saclay, 91405 Orsay Cédex, France
4Department of Mathematics, Simon Fraser University, 8888 University drive, Burnaby, BC, Canada V5A 1S6
5Centre de Génétique Moléculaire, UPR 3404 CNRS, Avenue de la Terrasse, Bât. 26, 91198 Gif-Sur-Yvette, France
6IGM, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay Cédex, France
7MAEM, CNRS UMR 7567, Université Henri Poincaré, 1 Boulevard des Aiguillettes, BP 239, 54506 Vandoeuvre-Les-Nancy Cédex, France
8LIFL, CNRS UMR 8022, Université Lille 1 and INRIA, 59655 Lille Cédex, France
9Inria Rhône-Alpes and LBBE, UMR 5558 CNRS, Université Claude Bernard, Bât. Grégor Mendel, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cédex, France

Received 28 September 2011; Accepted 22 February 2012

Academic Editor: Alejandro Schäffer

Copyright © 2012 Julien Allali et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. E. Zhu, F. Zhao, G. Xu et al., “MirTools: microRNA profiling and discovery based on high-throughput sequencing,” Nucleic Acids Research, vol. 38, no. 2, Article ID gkq393, pp. W392–W397, 2010. View at Publisher · View at Google Scholar · View at Scopus
  2. C. M. Sharma, S. Hoffmann, F. Darfeuille et al., “The primary transcriptome of the major human pathogen Helicobacter pylori,” Nature, vol. 464, no. 7286, pp. 250–255, 2010. View at Publisher · View at Google Scholar · View at Scopus
  3. I. Irnov, C. M. Sharma, J. Vogel, and W. C. Winkler, “Identification of regulatory RNAs in Bacillus subtilis,” Nucleic Acids Research, vol. 38, no. 19, Article ID gkq454, pp. 6637–6651, 2010. View at Publisher · View at Google Scholar · View at Scopus
  4. L. Childs, Z. Nikoloski, P. May, and D. Walther, “Identification and classification of ncRNA molecules using graph properties,” Nucleic Acids Research, vol. 37, no. 9, article e66, 2009. View at Publisher · View at Google Scholar · View at Scopus
  5. P. Menzel, J. Gorodkin, and P. F. Stadler, “The tedious task of finding homologous noncoding RNA genes,” RNA, vol. 15, no. 12, pp. 2075–2082, 2009. View at Publisher · View at Google Scholar · View at Scopus
  6. P. P. Gardner, J. Daub, J. Tate et al., “Rfam: wikipedia, clans and the “decimal” release,” Nucleic Acids Research, vol. 39, supplement 1, pp. D141–D145, 2011. View at Publisher · View at Google Scholar
  7. M. Andronescu, V. Bereg, H. H. Hoos, and A. Condon, “RNA STRAND: the RNA secondary structure and statistical analysis database,” BMC Bioinformatics, vol. 9, article 340, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. J. Allali and M. F. Sagot, “A multiple layer model to compare RNA secondary structures,” Software—Practice and Experience, vol. 38, no. 8, pp. 775–792, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. G. Blin, A. Denise, S. Dulucq, C. Herrbach, and H. Touzet, “Alignments of RNA structures,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 2, pp. 309–322, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. M. Höchsmann, T. Töller, R. Giegerich, and S. Kurtz, “Local similarity in RNA secondary structures.,” Proceedings/IEEE Computer Society Bioinformatics Conference, vol. 2, pp. 159–168, 2003. View at Google Scholar · View at Scopus
  11. V. Guignon, C. Chauve, and S. Hamel, “RNA StrAT: RNA Structure Analysis Toolkit,” in 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), p. D31, 2008.
  12. A. Ouangraoua, P. Ferraro, L. Tichit, and S. Dulucq, “Local similarity between quotiented ordered trees,” Journal of Discrete Algorithms, vol. 5, no. 1, pp. 23–35, 2007. View at Publisher · View at Google Scholar · View at Scopus
  13. N. R. Markham and M. Zuker, “DINAMelt web server for nucleic acid melting prediction,” Nucleic Acids Research, vol. 33, no. 2, pp. W577–W581, 2005. View at Publisher · View at Google Scholar · View at Scopus
  14. S. Janssen and R. Giegerich, “Faster computation of exact RNA shape probabilities,” Bioinformatics, vol. 26, no. 5, Article ID btq014, pp. 632–639, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. I. L. Hofacker, “Vienna RNA secondary structure server,” Nucleic Acids Research, vol. 31, no. 13, pp. 3429–3431, 2003. View at Publisher · View at Google Scholar · View at Scopus
  16. D. L. Wheeler, T. Barrett, D. A. Benson et al., “Database resources of the National Center for Biotechnology Information,” Nucleic Acids Research, vol. 35, no. 1, pp. D5–D12, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. E. A. Feingold, P. J. Good, M. S. Guyer et al., “The ENCODE (ENCyclopedia of DNA Elements) Project,” Science, vol. 306, no. 5696, pp. 636–640, 2004. View at Publisher · View at Google Scholar · View at Scopus
  18. Y. Ponty, M. Termier, and A. Denise, “GenRGenS: software for generating random genomic sequences and structures,” Bioinformatics, vol. 22, no. 12, pp. 1534–1535, 2006. View at Publisher · View at Google Scholar · View at Scopus
  19. B. A. Shapiro and K. Zhang, “Comparing multiple RNA secondary structures using tree comparisons,” Computer Applications in the Biosciences, vol. 6, no. 4, pp. 309–318, 1990. View at Google Scholar · View at Scopus
  20. C. Herrbach, “Etude algorithmique et statistique de la comparaison des structures secondaires d’ARN,” Ph.D. thesis, Université Bordeaux 1, 2007. View at Google Scholar
  21. K. Zhang and D. Shasha, “Simple fast algorithms for the editing distance between trees and related problems,” SIAM Journal on Computing, vol. 18, no. 6, pp. 1245–1262, 1989. View at Google Scholar · View at Scopus
  22. T. Jiang, L. Wang, and K. Zhang, “Alignment of trees—an alternative to tree edit,” Theoretical Computer Science, vol. 143, no. 1, pp. 137–148, 1995. View at Google Scholar · View at Scopus
  23. T. Jiang, G. Lin, B. Ma, and K. Zhang, “A general edit distance between RNA structures,” Journal of Computational Biology, vol. 9, no. 2, pp. 371–388, 2002. View at Publisher · View at Google Scholar · View at Scopus
  24. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus