James O. McInerney ,
Bioinformatics and Pharmacogenomics
Laboratory,
National University of Ireland,
Maynooth,
Co. Kildare,
Ireland.
Please cite:
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Purpose:
This program is designed to perform various tasks that are of use for
evaluating codon usage in a set of genes. You can get it to do some
simple things like calculate the number of observations of a particular
codon in a gene. Or you can do the same thing for the combined dataset.
You can also look at amino acid usage frequencies (again for each gene
or for the dataset as a whole). The program also produces a distance
matrix based on the similarity of codon usage in genes.
However, the most important feature of the program is its ability to use
multivariate analysis to look at variation in codon usage amongst
genes. Although it is popular to say that an organism has a particular
codon usage, it is now known that an organisms genes might have more than
one codon usage pattern and it is usually only by using a multivariate
analysis method that it is possible to ascertain the kinds of variation
contained within the data.