Comparative study of the nucleotide bias between the novel H1N1 and H5N1 subtypes of influenza A viruses using bioinformatics techniques

Journal of Microbiology and Biotechnology

Volumn 20, Issue 1, 2010, Pages 59-66

  Ahn, Insung ^a   Son, Hyeon Seok ^b  

^a Korea Institute of Science and Technology Information (KISTI)   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

Base composition; Genomics; H5N1 subtype; Influenza A virus; Novel H1N1 subtype

Indexed keywords

HEMAGGLUTININ; NUCLEOTIDE; SIALIDASE;

ARTICLE; BIOINFORMATICS; CODON USAGE; CONTROLLED STUDY; GENE SEQUENCE; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H5N1; NONHUMAN; NUCLEOTIDE SEQUENCE; PATTERN RECOGNITION; PHYLOGENY; SWINE; VIRUS GENE; VIRUS GENOME; VIRUS TRANSMISSION;

AVES; INFLUENZA A VIRUS; SUIDAE;

EID: 75849144708     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: 10.4014/jmb.0908.08004     Document Type: Article

References (21)

1. Ahn, I. and H. S. Son. 2006. Epidemiological comparisons of codon usage patterns among HIV-1 isolates from Asia, Europe, Africa and the Americas. Exp. Mol. Med. 38: 643-651.
2. Ahn, I. and H. S. Son. 2007. Comparative study of the hemagglutinin and neuraminidase genes of influenza A virus H3N2, H9N2, and H5N1 subtypes using bioinformatics techniques. Can. J. Microbiol. 53: 830-839.
3. Ahn, I., B. J. Jeong, S. E. Bae, J. Jung, and H. S. Son. 2006. Genomic analysis of influenza A viruses, including avian flu (H5N1) strains. Eur. J. Epidemiol. 21: 511-519.
4. Bao, Y., P. Bolotov, D. Dernovoy, B. Kiryutin, L. Zaslavsky, T. Tatusova, J. Ostell, and D. Lipman. 2008. The influenza virus resource at the National Center for Biotechnology Information. J. Virol. 82: 596-601.
5. Cary, N. C. 2004. SAS 9.1.2 Qualification Tools User's Guide, pp. 3-18. SAS Institute Inc., North Carolina.
6. Cox, N. J., R. A. Black, and A. P. Kendal. 1989. Pathways of evolution of influenza A (H1N1) viruses from 1977 to 1986 as determined by oligonucleotide mapping and sequencing studies. J. Gen. Virol. 70 (Pt 2): 299-313.
7. th Ed. Prentice Hall, Upper Saddle River, New Jersey.
8. Johnson, N. P. and J. Mueller. 2002. Updating the accounts: Global mortality of the 1918-1920 "Spanish" influenza pandemic. Bull. Hist. Med. 76: 105-115
9. th Ed. Prentice Hall, Upper Saddle River, New Jersey.
10. Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
11. Lynn, D. J., G. A. Singer, and D. A. Hickey. 2002. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30: 4272-4277.
12. Moriyama, E. N. and D. L. Hartl. 1993. Codon usage bias and base composition of nuclear genes in Drosophila. Genetics 134: 847-858.
13. Nelson, M. I., C. Viboud, L. Simonsen, R. T. Bennett, S. B. Griesemer, St. K. George, et al. 2008. Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog. 4: e1000012.
14. Perrière, G. and J. Thioulouse. 2002. Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res. 30: 4548-4555.
15. Sharp, P. M. and W. H. Li. 1986. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 14: 7737-7749.
16. Singer, G. A. and D. A. Hickey. 2003. Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 317: 39-47.
17. Suzuki, H., R. Saito, and M. Tomita. 2009. Measure of synonymous codon usage diversity among genes in bacteria. BMC Bioinformatics 10: 167.
18. Swofford, D. L. 1999. PAUP*. Phylogenetic Analysis using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, Massachusetts.
19. Taubenberger, J. K. and D. M. Morens. 2006. 1918 influenza: The mother of all pandemics. Emerg. Infect. Dis. 12: 15-22.
20. Vicario, S., E. N. Moriyama, and J. R. Powell. 2007. Codon usage in twelve species of Drosophila. BMC Evol. Biol. 7: 226.
21. Zhou, M. and X. Li. 2008. Analysis of synonymous codon usage patterns in different plant mitochondrial genomes. Mol. Biol. Rep. [Epub ahead of print.]