RNA Secondary Structure Analysis Using RNAstructure

David H. Mathews1

1 Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.6
DOI:  10.1002/0471250953.bi1206s46
Online Posting Date:  June, 2014
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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.

Keywords: RNA secondary structure prediction; free energy minimization; thermodynamics

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Table of Contents

  • Introduction
  • Basic Protocol 1: Predicting RNA Secondary Structure Using the RNAstructure Web Server
  • Alternate Protocol 1: Predicting Secondary Structure and Predicting Base‐Pair Probabilities with the RNAstructure Graphical User Interface
  • Basic Protocol 2: Predicting Binding Affinities of Oligonucleotides Complementary to an RNA Target with OligoWalk
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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Internet Resources
  The location of the Mathews lab Web site, where RNAstructure can be downloaded and the RNA‐structure Web servers can be accessed.
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