Using the RNAstructure Software Package to Predict Conserved RNA Structures

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 12.4
DOI:  10.1002/0471250953.bi1204s46
Online Posting Date:  June, 2014
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Abstract

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.

Keywords: RNA secondary structure prediction; RNA folding thermodynamics; RNA comparison

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Predicting a Structure Conserved in Three or More Sequences with the RNAstructure Web Server
  • Basic Protocol 2: Predicting a Structure Conserved in two Sequences with the RNAstructure Web Server
  • Alternate Protocol 1: Predicting a Structure Conserved in Three or more Sequences with TurboFold in the RNAstructure Graphical Interface
  • Alternate Protocol 2: Predicting a Structure Conserved in Two Sequences with Dynalign in the RNAstructure Graphical Interface
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
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