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Home >> Research >> Bioinformatics
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10. References

1. Grantham, R., Gautier, C., Gouy, M., Mercier, R. & Pave, A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8, r49-r62 (1980).
2. Ikemura, T. Correlation between the Abundance of Escherichia coli Transfer RNAs and the Occurance of the Respective Codons in its Protein Genes: A Proposal for a Synonymous Codon Choice that is Optimal for the E. coli Translational System. J. Mol. Biol. 151, 389-409 (1981).
3. Gouy, M. & Gautier, C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10, 7055-74 (1982).
4. Sharp, P. M., Averof, M., Lloyd, A. T., Matassi, G. & Peden, J. F. DNA sequence evolution: the sounds of silence. Philos Trans R Soc Lond B Biol Sci 349, 241-7 (1995).
5. Shields, D. C., Sharp, P. M., Higgins, D. G. & Wright, F. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol 5, 704-16 (1988).
6. Andersson, S. G. & Kurland, C. G. Codon preferences in free-living microorganisms. Microbiol Rev 54, 198-210 (1990).
7. Kanaya, S., Yamada, Y., Kudo, Y. & Ikemura, T. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238, 143-55 (1999).
8. Duret, L. Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 12, 640-9 (2002).
9. Peden, J. F. (1997). http://www.molbiol.ox.ac.uk/cu/
10. McInerney, J. O. GCUA: General Codon Usage Analysis. Bioinformatics 14, 372-373 (1998).
11. Greenacre, M. J. Theory and Applications of Correspondence Analysis (Academic Press, London, 1984).
12. Kohonen, T. Self-Organizing Maps (Springer-Verlag, Berlin, 1995).
13. Paulsen, I. T. et al. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A 99, 13148-53 (2002).
14. ORF Finder: http://www.ncbi.nlm.nih.gov/gorf/gorf.html
15. TIGR N. meningitidis page: ftp://ftp.tigr.org/pub/data/n_meningitidis/
16. TIGR Gene Attribute page: http://www.tigr.org/tigr-scripts/CMR2/gene_attribute_form.dbi

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