UNIT 12.11 Comparative ncRNA Gene and Structure Prediction Using Foldalign and FoldalignM

  1. Jakob Havgaard,
  2. Simranjeet Kaur,
  3. Jan Gorodkin

Published Online: 1 SEP 2012

DOI: 10.1002/0471250953.bi1211s39

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Havgaard, J., Kaur, S. and Gorodkin, J. 2012. Comparative ncRNA Gene and Structure Prediction Using Foldalign and FoldalignM. Current Protocols in Bioinformatics. 39:12.11:12.11.1–12.11.15.

Author Information

  1. Center for Non-Coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Copenhagen, Denmark

Publication History

  1. Published Online: 1 SEP 2012


This unit describes how to use Foldalign and FoldalignM to make structural alignments of non-protein-coding-RNA (ncRNA). These tools can be used to find new ncRNAs, to find the structure of novel ncRNAs, and to improve alignments for known ncRNAs. Curr. Protoc. Bioinform. 39:12.11.1-12.11.15. © 2012 by John Wiley & Sons, Inc.


  • ncRNA;
  • RNA structural alignment;
  • RNA structure prediction;
  • RNA multiple sequence alignment;
  • ncRNA gene finding;
  • non-coding RNA