Affiliations: Dipartimento di Scienze Biochimiche, Università
degli Studi di Firenze, viale Morgagni 50, 50134, Firenze, Italy | Dipartimento di Biologia Animale e Genetica "Leo
Pardi", Università degli Studi di Firenze, via Romana 17, 50125, Firenze,
Italy
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
