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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)

Summary

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 

Notes

Acknowledgments

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).

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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

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