  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.
