title: GenDecoder: genetic code prediction for metazoan mitochondria.
abstract: Although the majority of the organisms use the same genetic code to translate DNA, several variants have been described in a wide range of organisms, both in nuclear and organellar systems, many of them corresponding to metazoan mitochondria. These variants are usually found by comparative sequence analyses, either conducted manually or with the computer. Basically, when a particular codon in a query-species is linked to positions for which a specific amino acid is consistently found in other species, then that particular codon is expected to translate as that specific amino acid. Importantly, and despite the simplicity of this approach, there are no available tools to help predicting the genetic code of an organism. We present here GenDecoder, a web server for the characterization and prediction of mitochondrial genetic codes in animals. The analysis of automatic predictions for 681 metazoans aimed us to study some properties of the comparative method, in particular, the relationship among sequence conservation, taxonomic sampling and reliability of assignments. Overall, the method is highly precise (99%), although highly divergent organisms such as platyhelminths are more problematic. The GenDecoder web server is freely available from http://darwin.uvigo.es/software/gendecoder.html.
authors.affiliation: Departamento de Bioquímica, Genética, e Inmunología, Universidad de Vigo, 36310 Vigo, Spain. fabascal@uvigo.es
authors.forename: Federico
authors.initials: F
authors.lastname: Abascal
authors.forename: Rafael
authors.initials: R
authors.lastname: Zardoya
authors.forename: David
authors.initials: D
authors.lastname: Posada
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003062:Codon; D017124:Conserved Sequence; D019143:Evolution, Molecular; D050259:Genes, Mitochondrial; D020407:Internet; D014176:Protein Biosynthesis; D016415:Sequence Alignment; D017421:Sequence Analysis / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D003062:Codon