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Experiment-Assisted Secondary Structure Prediction with RNAstructure

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RNA Structure Determination

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1490))

Abstract

Experimental probing data can be used to improve the accuracy of RNA secondary structure prediction. The software package RNAstructure can take advantage of enzymatic cleavage data, FMN cleavage data, traditional chemical modification reactivity data, and SHAPE reactivity data for secondary structure modeling. This chapter provides protocols for using experimental probing data with RNAstructure to restrain or constrain RNA secondary structure prediction.

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Acknowledgement

This protocol was developed with the support of National Institutes of Health Grant R01GM076485 to D.H.M.

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Authors and Affiliations

  1. Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA

    Zhenjiang Zech Xu & David H. Mathews

  2. Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA

    Zhenjiang Zech Xu & David H. Mathews

  3. Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA

    David H. Mathews

Authors
  1. Zhenjiang Zech Xu
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  2. David H. Mathews
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Corresponding author

Correspondence to David H. Mathews .

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Editors and Affiliations

  1. Department of Chemistry and Center for RNA Biology, University of Rochester College of Arts and Sciences, Rochester, New York, USA

    Douglas H. Turner

  2. Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA

    David H. Mathews

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Xu, Z.Z., Mathews, D.H. (2016). Experiment-Assisted Secondary Structure Prediction with RNAstructure. In: Turner, D., Mathews, D. (eds) RNA Structure Determination. Methods in Molecular Biology, vol 1490. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6433-8_10

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  • DOI: https://doi.org/10.1007/978-1-4939-6433-8_10

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6431-4

  • Online ISBN: 978-1-4939-6433-8

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