Genetic code prediction for metazoan mitochondria with GenDecoder

Methods in Molecular Biology

Volumn 537, Issue , 2009, Pages 233-242

  Abascal, Federico ^a   Zardoya, Rafael ^b   Posada, David ^a  

^a UNIVERSITY OF VIGO   (Spain)

^b MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

Author keywords

bioinformatics; Genetic code; genomics; metazoan; mitochondria

Indexed keywords

ANIMALIA; METAZOA;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETIC CODE; GENETICS; METHODOLOGY; MITOCHONDRION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENETIC CODE; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 68049147464     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-251-9_11     Document Type: Article

References (17)

1. Crick, F. H. (1968) The origin of the genetic code J Mol Biol, 38, 367-79.
2. Di Giulio, M. (2005) The origin of the genetic code: theories and their relationships, a review. Biosystems 80, 175-84.
3. 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. (Pubitemid 33674769)
4. 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.
5. 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. (Pubitemid 32889539)
6. 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. (Pubitemid 34042283)
7. Knight, R. D., Landweber, L. F., and Yarus, M. (2001) How mitochondria redefine the code. J Mol Evol 53, 299-313. (Pubitemid 32889538)
8. Beagley, C. T., Okimoto, R., and Wolsten-holme, 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. (Pubitemid 28169021)
9. Barrell, B. G., Bankier, A. T., and Drouin, J. (1979) A different genetic code in human mitochondria. Nature 282, 189-94. (Pubitemid 10196509)
10. Telford, M. J., Herniou, E. A., Russell, R. B., and Littlewood, D. T. (2000) Changes in mitochondrial genetic codes as phyloge-netic characters: two examples from the flat-worms. Proc Natl Acad Sci USA 97, 11359-64.
11. Abascal, F., Zardoya, R., and Posada, D. (2006) GenDecoder: genetic code prediction for metazoan mitochondria. Nucleic Acids Res 34, W389-93. (Pubitemid 44529800)
12. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. (2004) GenBank: update. Nucleic Acids Res 32, D23-6. (Pubitemid 38081596)
13. Shannon, C. E. (1997) The mathematical theory of communication. 1963 MD Com-put 14, 306-17. (Pubitemid 127431633)
14. Wright, F. (1990) The 'effective number of codons' used in a gene. Gene 87, 23-9. (Pubitemid 20139850)
15. Clamp, M., Cuff, J., Searle, S. M., and Barton, G.J. (2004) The Jalview Java alignment editor. Bioinformatics 20, 426-7. (Pubitemid 38262778)
16. Lavrov, D. V., Brown, W. M., and Boore, J. L. (2004) Phylogenetic position of the Pen-tastomida and (pan)crustacean relationships. Proc Biol Sci 271, 537-44. (Pubitemid 38283149)
17. 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. (Pubitemid 32372943)