CAIcal: a combined set of tools to assess codon usage adaptation

Biol Direct. 2008 Sep 16:3:38. doi: 10.1186/1745-6150-3-38.


Background: The Codon Adaptation Index (CAI) was first developed to measure the synonymous codon usage bias for a DNA or RNA sequence. The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set.

Results: We describe here CAIcal, a web-server available at that includes a complete set of utilities related with the CAI. The server provides useful important features, such as the calculation and graphical representation of the CAI along either an individual sequence or a protein multiple sequence alignment translated to DNA. The automated calculation of CAI and its expected value is also included as one of the CAIcal tools. The software is also free to be downloaded as a stand alone application for local use.

Conclusion: The CAIcal server provides a complete set of tools to assess codon usage adaptation and to help in genome annotation.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological / genetics*
  • Base Sequence
  • Codon / genetics*
  • Evolution, Molecular*
  • Internet
  • Sequence Alignment
  • Sequence Analysis, DNA*
  • Software*


  • Codon