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DIAL (dihedral alignment) is a web-based tool for RNA sequence alignment based on structures. The DIAL algorithm does not require a reference genome and utilizes nucleotide sequence, dihedral angle, and nucleotide base-pairing similarity. The DIAL includes functions for Needleman-Wunsch (global), Smith-Waterman (local), motif search (global-semi global) alignments, and a viewer for 3-dimensional superposition of query and target.


Comparative genomics; Nucleic acid structure analysis; Data mining


  • Operation: Nucleic acid structure comparison; Local structure alignment; Structure visualisation; Global structure alignment
  • Software interface: Web user interface
  • Language: Python;C
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: The MIT License
  • Cost: Free
  • Version name: -
  • Maturity: Mature
  • Credit: National Science Foundation
  • Contact: clotelab _at_
  • Collection: -


Ferre F, Ponty Y, Lorenz WA, Clote P "DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities" Nucleic Acids Res. 2007 Jul;35(Web Server issue):W659-68. 10.1093/nar/gkm334. Epub 2007 Jun 13.
PMID: 17567620
PMCID: PMC1933154

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