MARNA

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Results: We describe a novel approach for multiple alignment of RNAs (MARNA) taking into consideration both the primary and the secondary structures. It is based on pairwise sequence–structure comparisons of RNAs. From these sequence–structure alignments, libraries of weighted alignment edges are generated. The weights reflect the sequential and structural conservation. For sequences whose secondary structures are missing, the libraries are generated by sampling low energy conformations. The libraries are then processed by the T-Coffee system, which is a consistency based multiple alignment method. Furthermore, we are able to extract a consensus-sequence and -structure from a multiple alignment. We have successfully tested MARNA on several datasets taken from the Rfam database. Availability: MARNA can be used online on our webpage www.bio.inf.uni-jena.de/Software/MARNA/index.html


References in zbMATH (referenced in 5 articles )

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  1. Fu, Haoyue; Yang, Lianping; Zhang, Xiangde: An RNA secondary structure prediction method based on minimum and suboptimal free energy structures (2015)
  2. Ouangraoua, Aïda; Guignon, Valentin; Hamel, Sylvie; Chauve, Cedric: A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes (2011)
  3. Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
  4. Bauer, Markus; Klau, Gunnar W.; Reinert, Knut: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization (2007) ioport
  5. Kruspe, Matthias; Stadler, Peter F.: Progressive multiple sequence alignments from triplets (2007) ioport