Unit

UNIT 12.8 RNA Secondary Structure Analysis Using The RNAshapes Package

  1. Jens Reeder1,
  2. Robert Giegerich2

Published Online: 1 JUN 2009

DOI: 10.1002/0471250953.bi1208s26

Lab Protocol Title

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Additional Information

How to Cite

Reeder, J. and Giegerich, R. 2009. RNA Secondary Structure Analysis Using The RNAshapes Package. Current Protocols in Bioinformatics. 26:12.8:12.8.1–12.8.17.

Author Information

  1. 1

    University of Colorado, Boulder, Colorado

  2. 2

    Bielefeld University, Bielefeld, Germany

Publication History

  1. Published Online: 1 JUN 2009
  2. Published Print: JUN 2009
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Abstract

This unit shows how to use the RNAshapes package for the prediction of the secondary structure of a single RNA sequence using either minimum free energy methods or weighted ensemble information. It also includes a protocol for the consensus prediction of a set of related sequences. Curr. Protoc. Bioinform. 26:12.8.1-12.8.17. © 2009 by John Wiley & Sons, Inc.

Keywords:

  • RNA secondary structure;
  • minimum free energy;
  • Boltzmann weighted ensemble;
  • consensus structure;
  • software package;
  • suboptimal folding space;
  • graphical user interface
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