cai

Function

Description

cai calculates the Codon Adaptation Index. This is a simple, effective measure of synonymous codon usage bias.

The CAI index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene sequence is calculated from the frequency of use of all codons in that gene sequence. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.

Usage

Command line arguments


Input file format

cai reads a nucleic acid sequence of a gene.

Output file format

cai writes the Codon Adaptation Index to the output file.

Data files

cai reads a reference codon usage table prepared from a set of genes which are known to be highly expressed.

The default codon usage table 'Eyeastcai.cut' is the standard set of Saccharomyces cerevisiae highly expressed gene codon frequiencies. Another table Eschpo_cai.cut was prepared from a set of Schizosaccharomyces pombe genes by Peter Rice for the S. pombe sequencing team at the Sanger Centre.

You should prepare your own codon usage table for your organism of interest.

Notes

None.

References

  1. Sharp PM., Li W-H. "The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications." Nucleic Acids Research 1987 vol 15, pp 1281-1295.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Author(s)

History

Target users

Comments