Summary
Riboswitches are vital components of many genomes. Covariance model searches for the characteristic architectures of riboswitch aptamer domains can be used to predict new examples of these structured RNAs. Since riboswitches generally function as cis-regulatory elements, examining the genomic contexts of these hits is critical for evaluating their biological relevance. With these two sources of comparative support, it is possible to identify riboswitches accurately from sequence information alone. Annotating riboswitches on a genomic scale enables more precise functions to be assigned to the proteins that they regulate, better defines their conserved aptamer structures by identifying diverged variants, and provides insight into how the genetic regulation of fundamental metabolic processes varies among species.
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Acknowledgments
The author would like to thank Zasha Weinberg for helpful comments on this protocol, discussions about filtering techniques, and contributing the script for generating HTML alignments; Chris Fields for his work on the BioPerl modules for parsing Stockholm alignments and interfacing with Infernal; Sean Eddy and colleagues for meticulously documenting and improving Infernal; Alex Bateman and Sam Griffiths-Jones for a generous look at the inner workings of the Rfam database; and especially Ronald Breaker and many other collaborators in his lab for converting bioinformatic fantasies into experimental realities.
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Barrick, J.E. (2009). Predicting Riboswitch Regulation on a Genomic Scale. In: Serganov, A. (eds) Riboswitches. Methods in Molecular Biology, vol 540. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-558-9_1
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DOI: https://doi.org/10.1007/978-1-59745-558-9_1
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