Abstract
There is a standard genetic code that is used by most organisms, but exceptions exist in which particular codons are translated with a different meaning, i.e., as a different amino acid. The characterization of the genetic code of an organism is hence a key step for properly analyzing and translating its protein-coding genes. Such characterization is particularly important in the case of metazoan mitochondrial genomes for two reasons: first, many variant codes occur in them and second, mitochondrial data is frequently used for evolutionary studies. Variant codes are usually found by comparative sequence analyses. Given a protein alignment, if a particular codon for a given species occurs at positions in which a particular amino acid is frequently found in other species, then the most likely hypothesis is that the codon is translated as that particular amino acid in that species. Previously, we have shown that this method can be very reliable provided that enough taxa and positions are included in the comparisons and have implemented it in the web-ser GenDecoder (http://darwin.uvigo.es/software/gendecoder.html).
In this chapter we describe the rationale of the method used by GenDecoder and its usage through worked examples, highlighting the potential problems that can arise during the analysis.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Crick, F. H. (1968) The origin of the genetic code J Mol Biol, 38, 367–79.
Di Giulio, M. (2005) The origin of the genetic code: theories and their relationships, a review. Biosystems 80, 175–84.
Knight, R. D., Freeland, S. J., and Landweber, L. F. (2001) Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet 2, 49–58.
Abascal, F., Posada, D., Knight, R. D., and Zardoya, R. (2006) Parallel evolution of the genetic code in arthropod mitochondrial genomes PLoS Biol 4, e127.
Yokobori, S., Suzuki, T., and Watanabe, K. (2001) Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity. J Mol Evol 53, 314–26.
Ivanov, V., Beniaminov, A., Mikheyev, A., and Minyat, E. (2001) A mechanism for stop codon recognition by the ribosome: a bioinformatic approach. RNA 7, 1683–92.
Knight, R. D., Landweber, L. F., and Yarus, M. (2001) How mitochondria redefine the code. J Mol Evol 53, 299–313.
Beagley, C. T., Okimoto, R., and Wolstenholme, D. R. (1998) The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code. Genetics 148, 1091–108.
Barrell, B. G., Bankier, A. T., and Drouin, J. (1979) A different genetic code in human mitochondria. Nature 282, 189–94.
Telford, M. J., Herniou, E. A., Russell, R. B., and Littlewood, D. T. (2000) Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms. Proc Natl Acad Sci USA 97, 11359–64.
Abascal, F., Zardoya, R., and Posada, D. (2006) GenDecoder: genetic code prediction for metazoan mitochondria. Nucleic Acids Res 34, W389–93.
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. (2004) GenBank: update. Nucleic Acids Res 32, D23–6.
Shannon, C. E. (1997) The mathematical theory of communication. 1963 MD Comput 14, 306–17.
Wright, F. (1990) The ‘effective number of codons’ used in a gene. Gene 87, 23–9.
Clamp, M., Cuff, J., Searle, S. M., and Barton, G. J. (2004) The Jalview Java alignment editor. Bioinformatics 20, 426–7.
Lavrov, D. V., Brown, W. M., and Boore, J. L. (2004) Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proc Biol Sci 271, 537–44.
von Nickisch-Rosenegk, M., Brown, W. M., and Boore, J. L. (2001) Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminths are Eutrochozoans Mol Biol Evol 18, 721–30.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Abascal, F., Zardoya, R., Posada, D. (2009). Genetic Code Prediction for Metazoan Mitochondria with GenDecoder. In: Posada, D. (eds) Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology, vol 537. Humana Press. https://doi.org/10.1007/978-1-59745-251-9_11
Download citation
DOI: https://doi.org/10.1007/978-1-59745-251-9_11
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-58829-910-9
Online ISBN: 978-1-59745-251-9
eBook Packages: Springer Protocols