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| Titel: |
The CAI Analyser Package: Inferring Gene Expressivity from Raw Genomic Data |
| Auteur: |
Ramazzotti, Matteo Brilli, Matteo Fani, Renato Manao, Giampaolo Degl'Innocenti, Donatella |
| Verschenen in: |
In silico biology |
| Paginering: | Jaargang 7 (2008) nr. 4-5 pagina's 507-526 |
| Jaar: |
2008-01-15 |
| Inhoud: |
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. |
| Uitgever: |
IOS Press |
| Bronbestand: |
Elektronische Wetenschappelijke Tijdschriften |
Details van artikel 16 van 16 gevonden artikelen
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