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Finding Instances of Riboswitches and Ribozymes by Homology Search of Structured RNA with Infernal

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Therapeutic Applications of Ribozymes and Riboswitches

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1103))

Abstract

In the genomics era, computational tools are essential to extract information from sequences and annotate them to allow easy access to genes. Fortunately, many of these tools are now part of standard pipelines. As a consequence, a cornucopia of genomic features is available in multiple databases. Nevertheless, as novel genomes are sequenced and new structured RNAs are discovered, homology searches and additional analyses need to be performed. In this chapter, we propose simple ways of finding instances of riboswitches and ribozymes in databases or in unannotated genomes, as well as ways of finding variants that deviate from the typical consensus.

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Acknowledgements

This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) discovery grant (RGPIN 418240-2012) and by a grant from The Banting Research Foundation to JP.

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Authors and Affiliations

  1. INRS-Institut Armand-Frappier, Laval, QC, Canada

    Amell El Korbi, Jonathan Ouellet, Mohammad Reza Naghdi & Jonathan Perreault

  2. Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC, Canada

    Amell El Korbi

Authors
  1. Amell El Korbi
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  2. Jonathan Ouellet
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  3. Mohammad Reza Naghdi
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  4. Jonathan Perreault
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Editor information

Editors and Affiliations

  1. Department of Biology, Université de Sherbrooke, Québec, Canada

    Daniel Lafontaine

  2. Départment de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada

    Audrey Dubé

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El Korbi, A., Ouellet, J., Naghdi, M.R., Perreault, J. (2014). Finding Instances of Riboswitches and Ribozymes by Homology Search of Structured RNA with Infernal. In: Lafontaine, D., Dubé, A. (eds) Therapeutic Applications of Ribozymes and Riboswitches. Methods in Molecular Biology, vol 1103. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-730-3_9

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  • DOI: https://doi.org/10.1007/978-1-62703-730-3_9

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-729-7

  • Online ISBN: 978-1-62703-730-3

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