Computational and Statistical Methodologies for ORFeome Primary Structure Analysis
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 WordsGenome 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).
- 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
- 21.Simonoff, J. (2003) Analyzing Categorical Data. Springer-Verlag, New York.Google Scholar
- 22.Everitt, B. S., Landau, S., and Leese, M. (2001) Cluster Analysis. Hodder Arnold, London, UK.Google Scholar