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RNA Structure Prediction, Analysis, and Design: An Introduction to Web-Based Tools

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Riboregulator Design and Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2518))

Abstract

Understanding RNA structure has become critical in the study of RNA in their roles as mediators of biological processes. To aid in these studies, computational algorithms that utilize thermodynamics have been developed to predict RNA secondary structure. Due to the importance of intermolecular interactions, the algorithms have been expanded to determine and predict RNA-RNA hybridization. This chapter discusses popular webservers with the tools for RNA secondary structure prediction, RNA-RNA hybridization, and design. We address key features that distinguish common-functioning programs and their purposes for the interests of the user. Ultimately, we hope this review elucidates web-based tools researchers may take advantage of in their investigations of RNA structure and function.

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Acknowledgments

R.A.I.Z. and C.H.P. were supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number TL4GM118977. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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  1. Authors Raphael Angelo I. Zambrano and Carmen Hernandez-Perez have equally contributed to this chapter.

Authors and Affiliations

  1. Department of Biology, California State University Northridge, Northridge, CA, USA

    Raphael Angelo I. Zambrano, Carmen Hernandez-Perez & Melissa K. Takahashi

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  1. Raphael Angelo I. Zambrano
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Correspondence to Melissa K. Takahashi .

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Editors and Affiliations

  1. Biosciences Department, Rice University, Houston, TX, USA

    James Chappell

  2. Department of Biology, California State University, Northridge, Northridge, CA, USA

    Melissa K. Takahashi

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Zambrano, R.A.I., Hernandez-Perez, C., Takahashi, M.K. (2022). RNA Structure Prediction, Analysis, and Design: An Introduction to Web-Based Tools. In: Chappell, J., Takahashi, M.K. (eds) Riboregulator Design and Analysis. Methods in Molecular Biology, vol 2518. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2421-0_15

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  • DOI: https://doi.org/10.1007/978-1-0716-2421-0_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2420-3

  • Online ISBN: 978-1-0716-2421-0

  • eBook Packages: Springer Protocols

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