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In Silico Biology 7, 0035 (2007); ©2007, Bioinformation Systems e.V.  

The CAI Analyser Package: inferring gene expressivity from raw genomic data

Matteo Ramazzotti1, Matteo Brilli2, Renato Fani2, Giampaolo Manao1 and Donatella Degl'Innocenti1*

1 Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, viale Morgagni 50, 50134, Firenze (Italy)
2 Dipartimento di Biologia Animale e Genetica "Leo Pardi", Università degli Studi di Firenze, via Romana 17, 50125, Firenze (Italy)

* Corresponding author

   Phone: +39-055-4598302;  Fax: +39-055-4598905

Edited by E. Wingender; received February 26, 2007; revised May 22, 2007; accepted June 21, 2007; published August 31, 2007


The Codon Adaptation Index (CAI) was introduced by Sharp and Li in 1987 to quantify codon usage similarities between a coding sequence and a set of reference sequences. When synonymous codons for a given amino acid exist, highly expressed genes seem to prefer some of them, according to tRNA abundance and thermodynamic issues. Some authors have described CAI-based methods to derive expressivity measures for all genes in a genome, in a computational framework.

Here we present the CAIAP (CAI Analyser Package), a platform independent package of computer programs allowing the calculation of the CAI and a deep study of gene expressivity from raw gene sequences. Our approach implements and optimizes a procedure to derive the reference sequences from whole genomes and use their codon usage for CAI estimation. Moreover, a set of analysis tools are provided to perform statistical analyses and therefore to give robustness to results. Objective: Our efforts were aimed to produce an easy-to-use and fully automatic set of programs specifically designed for the analysis of gene expressivity and inter-species comparisons on a great number of genomes. Moreover, the output integrates information coming from functional annotations of genes.

We are maintaining a web server storing our analyses for hundreds of genomes, allowing intergenomic comparison of data thanks to dedicated search engines. The CAIAP server is hosted at The programs (maintained as Perl scripts) are also available for download at the same location.

Keywords: gene expressivity, Codon Adaptation Index, intergenomic comparison, program package, web server