Most amino acids are specified by more than one codon. For example, the codons GCU, GCC, GCA and GCG all code for the amino acid Alanine and are therefore described as synonymous. However, genes of many organisms use these codons with different frequencies. The bias in synonymous codon usage has often been studied and discussed but there has been relatively little investigation of virus genomes and virtually none with plant viruses. We have developed the VirusCodon software to use the database and extract such data easily.
VirusCodon is a web-enabled Windows™ client application that uses the DPVweb database. One or more sequences of any of the viruses contained can easily be selected and the codon usage tables and other statistics generated for one or more genes from each sequence. In particular, the program calculates the GC content of each gene, the GC content of each codon position and the Effective Number of Codons used, which is a simple overall statistical measure of bias in synonymous codon usage (F. Wright, 1990, Gene 87, 23-29). The program greatly simplifies the work needed for analysis and we have already used the software to survey codon usage amongst all plant viruses. The program is available free and, provided that you have an active internet connection, it will run on your PC, using the DPVweb database at this web site.
The software is available as a zip file:
The program is largely intuitive but you can obtain full instructions here.
Please read the disclaimer before downloading or using the software.
These data have been generated using the VirusCodon program and are supplementary to a paper:
Codon usage bias amongst plant viruses.
Adams, MJ & Antoniw, JF (2004)
Archives of Virology, 149, 113-135.
They are provided here as PDF files: