RCDI/eRCDI: a web-server to estimate codon usage deoptimization

RCDI/eRCDI is a web application server that calculates the Relative Codon Deoptimization Index and a new expected value for the RCDI (eRCDI). The RCDI is used to estimate the similarity of the codon frequencies of a specific gene in comparison to a given reference genome. The eRCDI is determined by generating random sequences with similar G+C and amino acid composition to the input sequences and may be used as an indicator of the significance of the RCDI values. RCDI/eRCDI is freely available at http://genomes.urv.cat/CAIcal/RCDI webcite.This web server will be a useful tool for genome analysis, to understand host-virus phylogenetic relationships or to infer the potential host range of a virus and its replication strategy, as well as in experimental virology to ease the step of gene design for heterologous protein expression.Some studies suggest that viral genomes may acquire replicative fitness by selection in one of two ways. First, a codon usage optimized genome, as observed for viruses with high replication rates, such as Poliovirus [1,2]. Alternatively, selection might favour codon usage deoptimized genomes, as observed for viruses with low replication rates, such as Papillomaviruses [3,4]. However, some viruses may have both codon optimized and codon deoptimized genes which may be associated with a lytic or lysogenic phase respectively [5]. In addition, some authors propose that suboptimal codons may be used as a complementary strategy to develop polio vaccines [6-8].The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as a measure of codon deoptimization, by comparing the similarity in codon usage of a given gene to reference genome. Though the RCDI is a useful index for virus research, it has never been implemented for public use. In this article we describe the web-server RCDI/eRCDI that calculates the RCDI of a set of genes using the codon usage of a reference genome. However, the codon usage of a gene may be the product of