The RNA Virus Database

Belshaw, Robert; de Oliveira, Tulio; Markowitz, Sidney; Rambaut, Andrew

We provide amino acid sequences for all virus genes (or, more strictly, for all Open Reading Frames) plus complete translated genomes for each virus species (go to 'Proteins' on the toolbar of any virus species main page). The translated genomes are intended to facilitate phylogenetic analysis of more distantly related viruses (9) . One feature that makes annotation of RNA viruses difficult is that most species have some gene overlap (17) , i.e. where the same nucleotides code for two different genes by being read in two different frames. We, therefore, allow the user to select from three possible options for dealing with this feature: (i) have overlapped regions excised from the translated genome, (ii) have one only of any overlapped amino acid sequences represented or (iii) have all the amino acids sequences present, with overlapped sequences placed sequentially (and thus the nucleotides represented twice).