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Nucleic Acids Research 2006 34(Web Server issue):W389-W393; doi:10.1093/nar/gkl044
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Article

GenDecoder: genetic code prediction for metazoan mitochondria

Federico Abascal1,2,*, Rafael Zardoya2 and David Posada1

1 Departamento de Bioquímica, Genética, e Inmunología, Universidad de Vigo 36310 Vigo, Spain 2 Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales José Gutiérrez Abascal, 2, 28006 Madrid, Spain

*To whom correspondence should be addressed at Facultad de Biología, Campus Universitario, 36310 Vigo, Spain. Tel: +34 91 411 13 28 (ext 1129); Fax: +34 91 564 50 78; Email: fabascal{at}uvigo.es

Received January 11, 2006. Revised February 2, 2006. Accepted February 17, 2006.

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.


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