MultiSETTER - Multiple RNA Structure Similarity Algorithm
Recent advances in RNA research and a steady growth of available RNA structures call for bioinformatics methods for handling RNA structural data. Recently, we have introduced SETTER — a fast and accurate method for RNA pairwise structural alignment. In the present contribution we describe its extension for multiple RNA structure alignment called MultiSETTER. It combines SETTER’s decomposition of RNA structures into disjoint fragments with a well known multiple sequence alignment algorithm ClustalW adapted for the structural alignment. We demonstrate the validity of our approach on the task of automatic classification of RNA structures.
Keywordsstructural bioinformatics RNA tertiary structure structural similarity
Unable to display preview. Download preview PDF.
- 9.Tabei, Y., Kiryu, H., Kin, T., Asai, K.: A fast structural multiple alignment method for long RNA sequences. BMC Bioinformatics 9(1), 33 (2008)Google Scholar
- 15.Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4), 406–425 (1987)Google Scholar
- 17.Tamura, M., Hendrix, D.K., Klosterman, P.S., Schimmelman, N.R., Brenner, S.E., Holbrook, S.R.: SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res. 32(Database issue) (January 2004)Google Scholar