UNIT 12.6 RNA Secondary Structure Analysis Using RNAstructure

  1. David H. Mathews

Published Online: 17 JUN 2014

DOI: 10.1002/0471250953.bi1206s46

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Mathews, D. H. 2014. RNA Secondary Structure Analysis Using RNAstructure. Current Protocols in Bioinformatics. 46:12.6:12.6.1–12.6.25.

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


RNAstructure is a user-friendly program for the prediction and analysis of RNA secondary structure. It is available as a Web server, as a program with a graphical user interface, or as a set of command-line tools. The programs are available for Microsoft Windows, Macintosh OS X, or Linux. This unit provides protocols for RNA secondary structure prediction (using the Web server or the graphical user interface) and prediction of high-affinity oligonucleotide biding sites to a structured RNA target (using the graphical user interface). Curr. Protoc. Bioinform. 46:12.6.1-12.6.25. © 2014 by John Wiley & Sons, Inc.


  • RNA secondary structure prediction;
  • free energy minimization;
  • thermodynamics