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Bacterial Regulatory RNA pp 3–14Cite as

Bioinformatic Discovery of Bacterial Regulatory RNAs Using SIPHT

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 905))

Abstract

Diverse bacteria encode RNAs that are not translated into proteins but are instead involved in regulating a wide variety of cellular functions. Computational approaches have proven successful in identifying numerous regulatory RNAs in myriad bacterial species but the difficultly of implementing most of these approaches has limited their accessibility to many researchers. Moreover, few of these approaches provide annotations of predicted loci to guide downstream experimental validation and characterization. Here I describe the implementation of SIPHT, a web-accessible program that enables screens for putative loci encoding regulatory RNAs to be conducted in any of nearly 2,000 sequenced bacterial replicons. SIPHT identifies candidate loci by searching for regions of intergenic sequence conservation upstream of predicted intrinsic transcription terminators. Each locus is then annotated for numerous features that provide clues about its potential function and/or enable the most reliable candidates to be identified.

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Author information

Authors and Affiliations

  1. The Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Jonathan Livny

  2. Channing Laboratory, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

    Jonathan Livny

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  1. Jonathan Livny
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Corresponding author

Correspondence to Jonathan Livny .

Editor information

Editors and Affiliations

  1. , Dept. of Biochemistry and Molecular Biol, The Pennsylvania State University, Althouse Laboratory 0401, University Park, 16802, USA

    Kenneth C. Keiler

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Livny, J. (2012). Bioinformatic Discovery of Bacterial Regulatory RNAs Using SIPHT. In: Keiler, K. (eds) Bacterial Regulatory RNA. Methods in Molecular Biology, vol 905. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-949-5_1

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  • DOI: https://doi.org/10.1007/978-1-61779-949-5_1

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-948-8

  • Online ISBN: 978-1-61779-949-5

  • eBook Packages: Springer Protocols

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