Eur. Phys. J. B 65, 323-331 (2008)
https://doi.org/10.1140/epjb/e2008-00276-8

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

¹ Dipartimento di Fisica e Tecnologie Relative, Università di Palermo, Viale delle Scienze, 90128, Palermo, Italy
² Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA

Corresponding author: ^a mantegna@unipa.it

Received: 20 February 2008
Revised: 3 June 2008
Published online: 11 July 2008

Abstract

By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups, hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact, we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.