Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM

Curr Protoc Bioinformatics. 2012 Sep:Chapter 12:12.11.1-12.11.15. doi: 10.1002/0471250953.bi1211s39.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Nucleic Acid Conformation*
  • RNA, Untranslated
  • Sequence Alignment / methods*
  • Sequence Analysis, RNA


  • RNA, Untranslated