Energy-Based RNA Consensus Secondary Structure Prediction in Multiple Sequence Alignments

  • Stefan Washietl
  • Stephan H. Bernhart
  • Manolis Kellis
Protocol

Abstract

Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs.

Key words

RNA structure Consensus structure Structure prediction Functional RNA 

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Stefan Washietl
    • 1
  • Stephan H. Bernhart
    • 2
  • Manolis Kellis
    • 1
  1. 1.Computer Science and Artificial Intelligence LabMassachusetts Institute of TechnologyCambridgeUSA
  2. 2.Department of Computer Science and Interdisciplinary Center for BioinformaticsUniversity of LeipzigLeipzigGermany

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