UNIT 12.4 Using the RNAstructure Software Package to Predict Conserved RNA Structures

  1. David H. Mathews

Published Online: 17 JUN 2014

DOI: 10.1002/0471250953.bi1204s46

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Mathews, D. H. 2014. Using the RNAstructure Software Package to Predict Conserved RNA Structures. Current Protocols in Bioinformatics. 46:12.4:12.4.1–12.4.22.

Author Information

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

Publication History

  1. Published Online: 17 JUN 2014


The structures of many non-coding RNA (ncRNA) are conserved by evolution to a greater extent than their sequences. By predicting the conserved structure of two or more homologous sequences, the accuracy of secondary structure prediction can be improved as compared to structure prediction for a single sequence. This unit provides protocols for the use of four programs in the RNAstructure suite for prediction of conserved structures, Multilign, TurboFold, Dynalign, and PARTS. These programs can be run via Web servers, on the command line, or with graphical interfaces. Curr. Protoc. Bioinform. 46:12.4.1-12.4.22. © 2014 by John Wiley & Sons, Inc.


  • RNA secondary structure prediction;
  • RNA folding thermodynamics;
  • RNA comparison