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De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences

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RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1097))

Abstract

De novo discovery of “motifs” capturing the commonalities among related noncoding structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphasis on an approach based on the CMfinder program as a case study. Applications to genomic screens for novel de novo structured ncRNA s, including structured RNA elements in untranslated portions of protein-coding genes, are presented.

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Acknowledgements

This work is supported by the Danish Council for Independent Research (Technology and Production Sciences), the Danish Council for Strategic Research (Programme Commission on Strategic Growth Technologies), as well as the Danish Center for Scientific Computing.

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Authors and Affiliations

  1. Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA

    Walter L. Ruzzo

  2. Department of Computer Science & Engineering, University of Washington, Seattle, WA, 98105, USA

    Walter L. Ruzzo

  3. Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA

    Walter L. Ruzzo

  4. Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark

    Jan Gorodkin

  5. Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg C, Denmark

    Jan Gorodkin

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  1. Center for non-coding RNA in Technology and Health, IKVH University of Copenhagen, Frederiksberg, Denmark

    Jan Gorodkin

  2. University of Washington Dept. Computer Science & Engineering, Seattle, Washington, USA

    Walter L. Ruzzo

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Ruzzo, W.L., Gorodkin, J. (2014). De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences. In: Gorodkin, J., Ruzzo, W. (eds) RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Methods in Molecular Biology, vol 1097. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-709-9_15

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  • DOI: https://doi.org/10.1007/978-1-62703-709-9_15

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