Abstract
BackgroundThe Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome.FindingsRCDI/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.ConclusionsThis 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.
Highlights
The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome
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
Though the RCDI is a useful index for virus research, it has never been implemented for public use
Summary
The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome. Conclusions: 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. 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.
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