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Open Access Research

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

Pere Puigbò12*, Ignacio G Bravo3 and Santiago Garcia-Vallve1

Author Affiliations

1 Department of Biochemistry and Biotechnology, Rovira i Virgili University (URV). Campus Sescelades, c/Marcelli Domingo s/n, 43007 Tarragona, Spain

2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health. Bethesda, Maryland 20894, USA

3 Experimental Molecular Evolution, Institute for Evolution and Biodiversity, University of Muenster, Germany

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Biology Direct 2008, 3:38  doi:10.1186/1745-6150-3-38

Published: 16 September 2008

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 webcite 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 Purificación López-García, Dan Graur, Rob Knight and Shamil Sunyaev.