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

  • Amell El Korbi
  • Jonathan Ouellet
  • Mohammad Reza Naghdi
  • Jonathan Perreault
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

ncRNA Noncoding RNA Infernal Covariation Homology search RNA structure Secondary structure Riboswitches Ribozymes 

Notes

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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Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • Amell El Korbi
    • 1
    • 2
  • Jonathan Ouellet
    • 1
  • Mohammad Reza Naghdi
    • 1
  • Jonathan Perreault
    • 1
  1. 1.INRS-Institut Armand-FrappierLavalCanada
  2. 2.Institute for Research in Immunology and Cancer (IRIC)Université de MontréalMontréalCanada

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