Experiment-Assisted Secondary Structure Prediction with RNAstructure

Zhenjiang Zech Xu; David H Mathews

doi:10.1007/978-1-4939-6433-8_10

Experiment-Assisted Secondary Structure Prediction with RNAstructure

Methods Mol Biol. 2016;1490:163-76. doi: 10.1007/978-1-4939-6433-8_10.

Authors

Zhenjiang Zech Xu^{1

2}, David H Mathews^{3

4

5}

Affiliations

¹ Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA.
² Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA.
³ Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.
⁴ Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.
⁵ Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.

PMID: 27665598
DOI: 10.1007/978-1-4939-6433-8_10

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.

Keywords: Chemical modification data; RNA structure prediction; SHAPE; Thermodynamics.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Nucleic Acid Conformation*
RNA / chemistry*
Software*
Thermodynamics
User-Computer Interface
Web Browser

Substances

RNA

Grant support

R01 GM076485/GM/NIGMS NIH HHS/United States