title: Computational analysis of riboswitch-based regulation.
abstract: Advances in computational analysis of riboswitches in the last decade have contributed greatly to our understanding of riboswitch regulatory roles and mechanisms. Riboswitches were originally discovered as part of the sequence analysis of the 5'-untranslated region of mRNAs in the hope of finding novel gene regulatory sites, and the existence of structural RNAs appeared to be a spurious phenomenon. As more riboswitches were discovered, they illustrated the diversity and adaptability of these RNA regulatory sequences. The fact that a chemically monotonous molecule like RNA can discern a wide range of substrates and exert a variety of regulatory mechanisms was subsequently demonstrated in diverse genomes and has hastened the development of sophisticated algorithms for their analysis and prediction. In this review, we focus on some of the computational tools for riboswitch detection and secondary structure prediction. The study of this simple yet efficient form of gene regulation promises to provide a more complete picture of a world that RNA once dominated and allows rational design of artificial riboswitches. This article is part of a Special Issue entitled: Riboswitches.
authors.affiliation: Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA.
authors.forename: Eric I
authors.initials: EI
authors.lastname: Sun
authors.affiliation: Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA; A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia. Electronic address: rodionov@burnham.org.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Rodionov
keywords: Bacteria; Comparative genomics; Gene function; RNA regulatory motif; Regulon; Riboswitch