Computational and Statistical Methodologies for ORFeome Primary Structure Analysis

  • Gabriela Moura
  • Miguel Pinheiro
  • Adelaide Valente Freitas
  • José Luís Oliveira
  • Manuel A. S. Santos
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)


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.

Key Words

Genome ORFeome gene primary structure codon context codon usage 



This study was supported by FCT/FEDER project grant REF: POCI/BIA-MIC/55466/04. GM is supported by FCT (SFRH/BPD/7195/2001). MASS is an EMBO YIP and his work is supported by the FCT/POCI program and the Human Frontier Science Program (Grant RGP45/2005). AVF is member of the R&D Unit “Matemática e Aplicações,” University of Aveiro (through POCTI/FCT, cofinanced by FEDER).


  1. 1.
    Ogle, J. M. and Ramakrishnan, V. (2005) Structural insights into translational fidelity. Annu. Rev. Biochem. 74, 129–177.CrossRefPubMedGoogle Scholar
  2. 2.
    Irwin, B., Heck, J. D., and Hatfields, W. G. (1995) Codon pair utilization biases influence translational elongation step times. J. Biol. Chem. 270, 22, 801–22, 806.Google Scholar
  3. 3.
    Young, E. T., Sloan, J. S., and Riper, K. V. (2000) Trinucleotide repeats are clustered in regulatory genes in Saccharomyces cerevisiae. Genetics 154, 1053–1068.PubMedGoogle Scholar
  4. 4.
    Borstnik, B. and Pumpernik, D. (2002) Tandem repeats in protein coding regions of primate genes. Genome Res. 12, 909–915.CrossRefPubMedGoogle Scholar
  5. 5.
    Karlin, S., Brocchieri, L., Bergman, A., Mrazek, J., and Gentles, A. J. (2002) Amino acid runs in eukaryotic proteomes and disease associations. PNAS 99, 333–338.CrossRefPubMedGoogle Scholar
  6. 6.
    Flis, K., Hinzpeter, A., Edelman, A., and Kurlandzka, A. (2005) The functioning of mammalian CIC-2 chloride channel in Saccharomyces cerevisiae cells requires an increased level of Kha1p. Biochem. J. 390, 655–664.CrossRefPubMedGoogle Scholar
  7. 7.
    Folley, L. S. and Yarus, M. (1989) Codon contexts from weakly expressed genes reduce expression in vivo. J. Mol. Biol. 209, 359–378.CrossRefPubMedGoogle Scholar
  8. 8.
    Cliften, P., Fulton, R., Wilson, R., and Johnston, M. (2006) After the duplication: gene loss and adaptation in Saccharomyces genomes. Genetics 172, 863–872.CrossRefPubMedGoogle Scholar
  9. 9.
    Van de Lagemaat, L. N., Gagnier, L., Medstrand, P., and Mager, D. L. (2005) Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res. 15, 1243–1249.CrossRefPubMedGoogle Scholar
  10. 10.
    Lin, Y. W., Thi, D. A. D., Kuo, P. L., et al. (2005) Polymorphisms associated with the DAZ genes on the human Y chromosome. Genomics 86, 431–438.CrossRefPubMedGoogle Scholar
  11. 11.
    Chen, S. L., Lee, W., Hottes, A. K., and McAdams, H. H. (2004) Codon usage between genomes is constrained by genome-wide mutational processes. Proc. Natl. Acad. Sci. USA 101, 3480–3485.CrossRefPubMedGoogle Scholar
  12. 12.
    Berg, O. G. and Silva, P. J. (1997) Codon bias in Escherichia coli: the influence of codon context on mutation and selection. Nucleic Acids Res. 25, 1397–1404.CrossRefPubMedGoogle Scholar
  13. 13.
    Akashi, H. (1994) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136, 927–935.PubMedGoogle Scholar
  14. 14.
    Percudani, R. and Ottonello, S. (1999) Selection at the wobble position of codons read by the same tRNA in Saccharomyces cerevisiae. Mol. Biol. Evol. 16, 1752–1762.PubMedGoogle Scholar
  15. 15.
    Boycheva, S., Chkodrov, G., and Ivanov, I. (2003) Codon pairs in the genome of Escherichia coli. Bioinformatic 19, 987–998.CrossRefGoogle Scholar
  16. 16.
    Shah, A. A., Giddings, M. C., Parvaz, J. B., Gesteland, R. F., Atkins, J. F., and Ivanov, I. P. (2002) Computational identification of putative programmed translational frameshift sites. Bioinformatics 18, 1046–1053.CrossRefPubMedGoogle Scholar
  17. 17.
    Fedorov, A., Saxonov, S., and Gilbert, W. (2002) Regularities of context-dependent codon bias in eukaryotic genes. Nucleic Acids Res. 30, 1192–1197.CrossRefPubMedGoogle Scholar
  18. 18.
    Duan, J. and Antezana, M. A. (2003) Mammalial mutation pressure, synonymous codon choice, and mRNA degradation. J. Mol. Evol. 57, 649–701.CrossRefGoogle Scholar
  19. 19.
    Sharp, P. M. and Li, W. H. (1987) The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281–1295.CrossRefPubMedGoogle Scholar
  20. 20.
    Haberman, S. J. (1973) The analysis of residuals in cross-classified tables. Biometrics 29, 205–220.CrossRefGoogle Scholar
  21. 21.
    Simonoff, J. (2003) Analyzing Categorical Data. Springer-Verlag, New York.Google Scholar
  22. 22.
    Everitt, B. S., Landau, S., and Leese, M. (2001) Cluster Analysis. Hodder Arnold, London, UK.Google Scholar
  23. 23.
    Moura, G., Pinheiro, M., Silva, R., et al. (2005) Comparative context analysis of codon pairs on an ORFeome scale. Genome Biol. 6, R28.CrossRefPubMedGoogle Scholar
  24. 24.
    Wright, F. (1990) The ‘effective number of codons’ used in a gene. Gene 87, 23–29.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Gabriela Moura
    • 1
  • Miguel Pinheiro
    • 2
  • Adelaide Valente Freitas
    • 3
  • José Luís Oliveira
    • 4
  • Manuel A. S. Santos
    • 5
  1. 1.Department of BiologyUniversity of AveiroPortugal
  2. 2.Department of BiologyUniversity of AveiroPortugal
  3. 3.Department of BiologyUniversity of AveiroPortugal
  4. 4.Department of BiologyUniversity of AveiroPortugal
  5. 5.Department of BiologyUniversity of AveiroPortugal

Personalised recommendations