Deciphering viral RNA structure with ViennaRNA

Abstract

The ability of RNA to fold into intricate structures in 2D and 3D is exploited by viruses to mediate tropism. Therefore, a deep understanding of RNA structure formation is crucial for the emerging field of virus bioinformatics. The ViennaRNA Package comes with a rich portfolio of tools to analyze RNA folding and the traits that are associated with particular folds. Single sequence modeling from thermodynamic principles and comparative studies of RNA structure provide a powerful approach to assess evolutionary conservation of viral genomes. This presentation introduces the ViennaRNA Package and examines how it can help virologists to address RNA structuredness by the example of a recent project that was focused around the characterization of alternative RNA structure conservation in different subtypes of tick-borne encephalitis virus (TBEV).