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

Abstract

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 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.

Figure 1

Schematic representation of the options available in the CAIcal server. Using a combination of three inputs (DNA or RNA sequences, a codon usage reference table and/or a protein alignment), the server calculates gene parameters such as %G+C, Relative Synonymous Codon Usage (RSCU) and Effective Number of Codons (ENc), the CAI for one or more DNA or RNA sequences and an expected CAI and represents the CAI along a DNA sequence or in a protein multialignment translated to DNA.

Figure 2

Representation of the CAI, calculated using the human mean codon usage as a reference set, in the DNA sequence that encodes HPV63 E2 and E4. Part A represents the reading frame that encodes E2. Part B represents the same HPV63 genome fragment that encodes E2, but in the reading frame +1, which contains E4. The grey line in B represents the fragment of HPV63 E4 homologous to the closely related HPV1 E4. The black line in B represents the stretch also annotated as HPV63 E4, but which lacks homology with HPV1 E4. Note that the initial E4 region from HPV63, which is not homologous to the HPV1 gene, has an extremely low CAI, which suggests a wrong annotation for the E4 gene in HPV63. This figure was obtained using the output of the calculation of CAI along a sequence of the CAIcal server, with a window length of 11 and a window step of 5.