Please note:
MARNA is not maintained anymore since 2005. For the task of multiple sequence-structure RNA alignment the more advanced tool LocARNA is superseding MARNA (check fixed structure input in LocARNA help page).

MARNA is a multiple alignment of RNAs taking into consideration both the primary sequence and the secondary structure. It is based on pairwise comparisons using costs of edit operations. The edit operations can be divided into edit operations on arcs and edit operations on bases. Additionally, MARNA predicts a consensus sequence as well as a consensus structure.

For articles describing the tool and webserver refer to the reference section below. Please cite us when using our tools.
For more information check the help page.

• Sven Siebert and Rolf Backofen
  MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
  Bioinformatics 2005, Volume 21, Issue 16, 3352-3359
  
• Sven Siebert and Rolf Backofen
  MARNA: A server for multiple alignment of RNAs
  In Proc. of German Conference on Bioinformatics (GCB'03), pages 135-140, October 2003
  
• Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
  Freiburg RNA tools: a central online resource for RNA-focused research and teaching
  Nucleic Acids Research, 46(W1), W25-W29, 2018.