title: The CAI Analyser Package: inferring gene expressivity from raw genomic data.
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.
authors.affiliation: Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, viale Morgagni 50, 50134, Firenze, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Ramazzotti
authors.forename: Matteo
authors.initials: M
authors.lastname: Brilli
authors.forename: Renato
authors.initials: R
authors.lastname: Fani
authors.forename: Giampaolo
authors.initials: G
authors.lastname: Manao
authors.forename: Donatella
authors.initials: D
authors.lastname: Degl'innocenti
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D002876:Chromosomes, Bacterial / Q000235:genetics; D003062:Codon / Q000235:genetics*; D048168:Escherichia coli K12 / Q000235:genetics; D015870:Gene Expression / Q000235:genetics*; D020407:Internet; D012269:Ribosomal Proteins / Q000096:biosynthesis; D012984:Software
chemical_list: D003062:Codon; D012269:Ribosomal Proteins