Finding instances of riboswitches and ribozymes by homology search of structured RNA with Infernal.

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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Submitted on : Wednesday, March 25, 2015 - 3:17:48 PM
Last modification on : Monday, October 8, 2018 - 5:44:05 PM

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Amell El Korbi, Jonathan Ouellet, Mohammad Reza Naghdi, Jonathan Perreault. Finding instances of riboswitches and ribozymes by homology search of structured RNA with Infernal.. Methods in Molecular Biology, Humana Press/Springer Imprint, 2014, 1103, pp.113-26. ⟨10.1007/978-1-62703-730-3_9⟩. ⟨pasteur-01135590⟩

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