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Sequence-based identification of 3D structural modules in RNA with RMDetect

Nature Methods volume 8, pages 513–519 (2011)Cite this article

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Abstract

Structural RNA modules, sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs, have central roles as architectural organizers and sites of ligand binding in RNA molecules, and are recurrently observed in RNA families throughout the phylogeny. Here we describe a computational tool, RNA three-dimensional (3D) modules detection, or RMDetect, for identifying known 3D structural modules in single and multiple RNA sequences in the absence of any other information. Currently, four modules can be searched for: G-bulge loop, kink-turn, C-loop and tandem-GA loop. In control test sequences we found all of the known modules with a false discovery rate of 0.23. Scanning through 1,444 publicly available alignments, we identified 21 yet unreported modules and 141 known modules. RMDetect can be used to refine RNA 2D structure, assemble RNA 3D models, and search and annotate structured RNAs in genomic data.

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Figure 1: Details of the analyzed RNA structural modules.
Figure 2: Steps of single- and multiple-sequence search algorithms.
Figure 3: Examples of the newly predicted modules.

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Acknowledgements

We thank R. Backofen for useful suggestions. J.A.C. is supported by the Ph.D. Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA and Fundação para a Ciência e Tecnologia; SFRH/BD/33528/2008).

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Authors and Affiliations

  1. Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France

    José Almeida Cruz & Eric Westhof

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  1. José Almeida Cruz
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  2. Eric Westhof
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Contributions

J.A.C. conceived the algorithms, performed the computations and wrote the manuscript. E.W. conceived the research and wrote the manuscript.

Corresponding author

Correspondence to Eric Westhof.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10, Supplementary Table 1, Supplementary Notes 1–6, Supplementary Data 1–3 (PDF 8744 kb)

Supplementary Software 1

Rmdetect (ZIP 940 kb)

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Cruz, J., Westhof, E. Sequence-based identification of 3D structural modules in RNA with RMDetect. Nat Methods 8, 513–519 (2011). https://doi.org/10.1038/nmeth.1603

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