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Computational Identification of sRNA Targets

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Bacterial Regulatory RNA

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

Abstract

Many small noncoding RNAs (sRNAs) in bacteria act as posttranscriptional regulators by base pairing to their message targets. TargetRNA is a program that predicts the targets of a sRNA by identifying messages with significant potential to base pair with the sRNA. Since base pairing potential alone is insufficient to accurately identify sRNA targets, TargetRNA integrates several additional features of RNA interactions when predicting regulatory targets of a sRNA. In this chapter, we provide a detailed guide on how to use TargetRNA to identify targets of sRNA regulation.

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Author information

Authors and Affiliations

  1. Computer Science Department, Wellesley College, Wellesley, MA, USA

    Brian Tjaden

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  1. Brian Tjaden
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Corresponding author

Correspondence to Brian Tjaden .

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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Tjaden, B. (2012). Computational Identification of sRNA Targets. 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_14

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  • DOI: https://doi.org/10.1007/978-1-61779-949-5_14

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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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