The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3. doi: 10.1093/nar/gki473.


Foldalign is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of foldalign. The server can be used to scan two sequences for a common structural RNA motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. The web server can be accessed at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computer Graphics
  • Internet
  • Nucleic Acid Conformation
  • RNA / chemistry*
  • Sequence Alignment / methods*
  • Sequence Analysis, RNA / methods*
  • Software*
  • User-Computer Interface


  • RNA