title: Computational and statistical methodologies for ORFeome primary structure analysis.
abstract: Codon usage and context are biased in open reading frames (ORFs) of most genomes. Codon usage is largely influenced by biased genome G+C pressure, in particular in prokaryotes, but the general rules that govern the evolution of codon context remain largely elusive. To shed new light into this question, we have developed computational, statistical, and graphical tools for analysis of codon context on an ORFeome wide scale. Here, we describe these methodologies in detail and show how they can be used for analysis of ORFs of any genome sequenced.
authors.affiliation: Department of Biology, University of Aveiro.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Moura
authors.forename: Miguel
authors.initials: M
authors.lastname: Pinheiro
authors.forename: Adelaide Valente
authors.initials: AV
authors.lastname: Freitas
authors.forename: José Luís
authors.initials: JL
authors.lastname: Oliveira
authors.forename: Manuel A S
authors.initials: MA
authors.lastname: Santos
mesh_terms: D003062:Codon; D016678:Genome; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D012984:Software
chemical_list: D003062:Codon