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

Experiment-Assisted Secondary Structure Prediction with RNAstructure.

Xu ZZ1,2, Mathews DH3,4,5.

Author information

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.

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

PMID:
27665598
DOI:
10.1007/978-1-4939-6433-8_10
[Indexed for MEDLINE]

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