A new informatics method for measuring synonymous codon usage bias

Intelligent Engineering Systems Through Artificial Neural Networks

Volumn 13, Issue , 2003, Pages 1011-1018

  Wan, Xiufeng ^a   Zhou, Jizhong ^a   Xu, Dong ^b  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CODON ADAPTATION INDEX (CAI); CODON USAGE; INFORMATICS; SACHAROMYCES CEREVISIAE;

AMINO ACIDS; COMPUTATION THEORY; DATA REDUCTION; DNA; ESCHERICHIA COLI; INFORMATION THEORY; PROTEINS;

GENES;

EID: 2442476605     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (28)

1. Aota, S. and Ikemura, T. (1986) Diversity in G + C content at the third position of codons in vertebrate genes and its cause. Nucleic Acids Res., 14, 6345-6355.
2. nd edition. The University of Chicago Press, Chicago.
3. Coghlan, A., and K. H. Wolfe. (2000) Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast, 16, 1131-1145.
4. Cosmi, C. C., Ragosta, V., and Macchiato, M. F. (1990) Characterization of nucleotide sequences using maximum entropy techniques. J. Theor. Biol., 147, 423-432.
5. D'Onofrio, G., Mouchiroud, D., Aissani, B., Gautier, C. and Bernardi, G. (1991) Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J. Mol. Evol., 32, 504-510.
6. Gatlin, L. L. (1972) Information Theory and the Living System. Columbia University Press.
7. Grantham, R., Gautier, C. and Gouy, M. (1980) Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res., 8, 1893-1912.
8. Gouy, M. and Gautier, C. (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res., 10, 7055-7074.
9. Ikemura, T. (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2, 13-34.
10. Kanaya, S., Yamada, Y., Kudo, Y. and Ikemura, T. (1999) 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, 143-155.
11. Karlin, S., Mrazek, J. and Campbell, A. M. (1988a) Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol., 29, 1341-1355.
12. Karlin, S., Campbell, A. M. and Mrazek, J. (1998b) Comparative DNA analysis across diverse genomes. Annu. Rev. Genet., 32, 185-225.
13. Layzer, D. (1977) Information in cosmology, physics and biology. Int. J. Quantum Chem., 12 (suppl. 1), 185-195.
14. McLachlan, A. D., Staden, R. and Boswell, D. R. (1984) A method for measuring the non-random bias of a codon usage table. Nucleic Acids Res., 12, 9567-9575.
15. Murray, E. E., Lotzer, J. and Eberle, M. (1989) Codon usage in plant genes. Nucleic Acids Res., 17, 477-498.
16. Peden, J. F. (1999) Analysis of codon usage, Ph.D. Thesis, University of Nottingham.
17. Sharp, P. M., Cowe, E., Higgins, D. G., Shields, D. C., Wolfe, K. H. and Wright, F. (1988) Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res., 16, 8207-8211.
18. Sharp, P. M. and Li, W. H. (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol., 24, 28-38.
19. Sharp, P. M., Tuohy, T. M., and Mosurski, K.R. (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14, 5125-5143.
20. 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.
21. Shields, D. C., Sharp, P. M., Higgins, D. G. and Wright, F. (1988) "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol., 5, 704-716.
22. Shileds, D. C. and Sharp, P. M. (1987) Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acid Res., 15, 8023-8040.
23. Smith, N. G. C. and Eyre-Walker, A. (2001) Why are translationally sub-optimal synonymous codons used in Esherichia coli? J. Mol. Evol., 53, 225-236.
24. Tatusov, R. L., Koonin, E. V. and Lipman, D. J. (1997) A genomic perspective on protein families. Science, 278, 631-637.
25. Tatusov, R. L., Galperin, M. Y., Natale, D. A. and Koonin, E. V. (2002) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res., 28, 33-36.
26. VanBogelen, R. A., Olson, E. R., Wanner, B. L., and Neidhardt, F. C. (1996) Global analysis of proteins synthesized during phosphorus restriction in Escherichia coli. J. Bacterial., 178, 4344-4366.
27. Velculescu, V. E., L. Zhang, W. Zhou, J. Volgelstein, M. A. Basrai, D. E. Jr. Bassett, P. Hieter, B. Vogelstein, K. W. Kinzler. (1997) Characterization of the yeast transcriptome. Cell, 88, 243-251.
28. Zeeberg, B. (2002) Shannon information theoretic computation of synonymous codon usage biases in coding regions of human and mouse genomes. Genome Res., 12, 944-955.