MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W14-8. doi: 10.1093/nar/gkn321. Epub 2008 May 30.


MAGNOLIA is a new software for multiple alignment of nucleic acid sequences, which are recognized to be hard to align. The idea is that the multiple alignment process should be improved by taking into account the putative function of the sequences. In this perspective, MAGNOLIA is especially designed for sequences that are intended to be either protein-coding or structural RNAs. It extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern between sequences before aligning them. The alignment step then incorporates this information to achieve higher accuracy. The website is available at

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Internet
  • Nucleic Acid Conformation
  • Proteins / genetics*
  • RNA, Untranslated / chemistry*
  • RNA, Untranslated / genetics
  • Sequence Alignment / methods*
  • Sequence Analysis, RNA*
  • Software*


  • Proteins
  • RNA, Untranslated