Automated motif extraction and classification in RNA tertiary structures

  1. Mahassine Djelloul1 and
  2. Alain Denise1,2
  1. 1Laboratoire de Recherche en Informatique, Université Paris-Sud 11 and CNRS, 91405 Orsay Cedex, France
  2. 2Institut de Génétique et Microbiologie, Université Paris-Sud 11 and CNRS, 91405 Orsay Cedex, France

Abstract

We used a novel graph-based approach to extract RNA tertiary motifs. We cataloged them all and clustered them using an innovative graph similarity measure. We applied our method to three widely studied structures: Haloarcula marismortui 50S (H.m 50S), Escherichia coli 50S (E. coli 50S), and Thermus thermophilus 16S (T.th 16S) RNAs. We identified 10 known motifs without any prior knowledge of their shapes or positions. We additionally identified four putative new motifs.

Keywords

Footnotes

  • Reprint requests to: Alain Denise, Laboratoire de Recherche en Informatique, Université Paris-Sud 11 and CNRS, 91405 Orsay Cedex, France; e-mail: Alain.Denise{at}lri.fr; fax: 33-1-69156586.

  • Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.1061108.

    • Received March 5, 2008.
    • Accepted August 15, 2008.
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  1. Published in Advance October 28, 2008, doi: 10.1261/rna.1061108 RNA 14: 2489-2497 Copyright © 2008 RNA Society

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