Abstract

- Article -

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

Email: donatella.deglinnocenti@unifi.it
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

Abstract

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 www4.unifi.it/scibio/bioinfo/caiap/html. 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