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.
The CAI Analyser Package: inferring gene expressivity from raw genomic data / M. Ramazzotti, M. Brilli, R. Fani, G. Manao, D. Degl'Innocenti. - In: IN SILICO BIOLOGY. - ISSN 1386-6338. - 7:4-5(2007), pp. 507-526.
|Titolo:||The CAI Analyser Package: inferring gene expressivity from raw genomic data|
|Parole Chiave:||Gene expressivity, Codon Adaptation Index, intergenomic comparison, program package, web server|
|Settore Scientifico Disciplinare:||Settore BIO/10 - Biochimica|
Settore BIO/11 - Biologia Molecolare
Settore BIO/19 - Microbiologia Generale
|Data di pubblicazione:||2007|
|Appare nelle tipologie:||01 - Articolo su periodico|