viRNA: A collection of conserved viral RNA structures

Michael T. Wolfinger^1,2

_{¹Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
²Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria}

This repository is intended to provide a (not necessarily complete) collection of structural multiple sequence alignments of evolutionary conserved RNA structures in viruses. Currently, specific ecologic groups of flaviviruses are covered.

Each alignment of viral sequences represents a particular RNA family of structurally homologous entities and has been built either from known RNA families or derived de-novo by comparative genomics. All alignments are in Stockholm format, which allows easy construction of Infernal covariance models.

While some of the alignments are also available though the Rfam database, several alignments provided here have been specifically built for particular viral species or groups. This allows for a fine-grained characterization and comparison of conserved RNA elements in different viruses, as outlined in the below publications. The Stockholm alignments featured here were constructed from NCBI Genbank dumps of all available viruses of the respective genus available at the time of element construction. As such, the virRNA alignments represent the entire sequence diversity associated with formation of a particular RNA element, thereby accounting for covariation information observed within a virus (species), serological group, or ecological group.

If you use data provided in this repository in your own work please link back to this site and cite the following publications - Thank you!

• Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology
  Lena S. Kutschera, Michael T. Wolfinger
  Virus Evol. (8):1 veac051 (2022) PDF | doi:10.1093/ve/veac051

• Functional RNA Structures in the 3’UTR of Mosquito-Borne Flaviviruses
  Michael T. Wolfinger, Roman Ochsenreiter, Ivo L. Hofacker
  In Virus Bioinformatics pp 65-100; Chapman and Hall/CRC (2021) Preprint PDF | doi:10.1201/9781003097679-5

• Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses
  Roman Ochsenreiter, Ivo L. Hofacker, Michael T. Wolfinger
  Viruses 11(3):298 (2019) PDF | doi:10.3390/v11030298