NEMrRNA is a database for secondary structure information of ribosomal RNA molecules in dot-bracket structural format. The database is developed to support phylogenetic studies of nematodes.

Phylogenetic studies using ribosomal RNA sequences often ignore that this molecule forms complex secondary and tertiary structures mediated by base pairing between sometimes distant regions of the molecule. Knowledge of RNA secondary structure is becoming increasingly important in assisting phylogenetic analysis through three main approaches. First, secondary structure is used to identify homologous positions for sets of nucleotides and sequence regions, which are otherwise difficult to determine using multiple alignment algorithms. Second, secondary structure can be used as an additional source of data incorporating both structural and morphometric parameters of rRNA molecules. Third, secondary structure is used for selecting increasingly appropriate models of evolution. It has been shown in many studies that the mode of evolution within helical regions of rRNA is via compensatory or semi-compensatory mutations, and thus, the evolution of bases in structurally related positions is highly dependent.

Reference: Subbotin, S.A., Sturhan, D., Vovlas, N., Castillo, P., Tanyi Tambe, J., Moens, M. and Baldwin, J.G. (2006). Application of secondary structure model of rRNA for phylogeny: D2-D3 expansion segments of the LSU gene of plant-parasitic nematodes from the family Hoplolaimidae Filipjev, 1934. Molecular Phylogenetics and Evolution 43: 881-890.

Acknowledgements. The assistance of Alex Patel in designing the database is greatly appreciated. The support from the US National Science Foundation grant DEB 0228692 and USDA grant 2005-00903 are acknowledged.

Programs for visualization of RNA secondary structure:

    PseudoViewer is a program for visualizing large-scale RNA secondary structures with pseudoknots of any type.


    jViz.Rna is a multi-platform visualization tool capable of displaying RNA secondary structures.


    RnaViz is a user-friendly, portable program for producing publication-quality secondary structure drawings of RNA molecules.

This page is maintained by Sergei A. Subbotin