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

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 http://genomes.urv.es/CAIcal 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 standalone 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. Reviewers: This article was reviewed by Purificacion Lopez-Garc a, Dan Graur, Rob Knight and Shamil Sunyaev.