Development and public release of a comprehensive hepatitis virus database

Hepatology Research

Volumn 38, Issue 3, 2008, Pages 234-243

  Shin I , Tadasu ^a   Tanaka, Yasuhito ^a   Tateno, Yoshio ^b   Mizokami, Masashi ^a  

^a NAGOYA CITY UNIVERSITY GRADUATE SCHOOL OF MEDICAL SCIENCES   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Database; Genome; Hepatitis virus; Phylogenetic relationships

Indexed keywords

ARTICLE; GENE LOCUS; GENE SEQUENCE; GENETIC DATABASE; GENOME ANALYSIS; GENOTYPE; HEPATITIS B; HEPATITIS B VIRUS; HEPATITIS C; HEPATITIS C VIRUS; HEPATITIS E; HEPATITIS E VIRUS; INFORMATION RETRIEVAL; INTERNET; MEDICAL INFORMATION; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE DATABASE; UNINDEXED SEQUENCE; VIRUS GENE; VIRUS GENOME;

EID: 38849113798     PISSN: 13866346     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1872-034X.2007.00262.x     Document Type: Article

References (24)

1. Poynard T, Yuen MF, Ratziu V, Lai CL. Viral hepatitis C. Lancet 2003; 362: 2095-100.
2. Afdhal NH. The natural history of hepatitis C. Semin Liver Dis 2004; 24 (Suppl 2): 3-8.
3. Choo QL, Richman KH, Han JH et al. Genetic organization and diversity of the hepatitis C virus. Proc Natl Acad Sci USA 1991; 88: 2451-5.
4. Robertson B, Myers G, Howard C et al. Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization. International Committee on Virus Taxonomy. Arch Virol 1998; 143: 2493-503.
5. Martinot-Peignoux M, Marcellin P, Pouteau M et al. Pretreatment serum hepatitis C virus RNA levels and hepatitis C virus genotype are the main and independent prognostic factors of sustained response to interferon alpha therapy in chronic hepatitis C. Hepatology 1995; 22: 1050-6.
6. Kao JH, Chen DS. Global control of hepatitis B virus infection. Lancet Infect Dis 2002; 2: 395-403.
7. Custer B, Sullivan SD, Hazlet TK, Iloeje U, Veenstra DL, Kowdley KV. Global epidemiology of hepatitis B virus. J Clin Gastroenterol 2004; 38: S158-68.
8. Hou J, Liu Z, Gu F, Epidemiology and prevention of hepatitis B virus infection. Int J Med Sci 2005; 2: 50-7.
9. Miyakawa Y, Mizokami M. Classifying Hepatitis B virus genotypes. Intervirology 2003; 46: 329-38.
10. Reyes GR, Purdy MA, Kim JP et al. Isolation of cDNA from the virus responsible for enterically transmitted non-A, non-B hepatitis. Science 1990; 247: 1336-9.
11. Tam AW, Smith MM, Guerra ME et al. Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome. Virology 1991; 185: 120-31.
12. Okubo K, Sugawara H, Gojobori T, Tateno Y. DDBJ in preparation for overview of research activities behind data submissions. Nucleic Acids Res 2006; 34: D6-9.
13. Kolykhalov AA, Agapov EV, Blight KJ, Mihalik K, Feinstone SM, Rice CM. Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA. Science 1997; 277: 570-4.
14. Kuiken C, Combet C, Bukh J et al. A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes. Hepatology 2006; 44: 1355-61.
15. Pearson WR, Lipman DJ. Improved tools for biological sequence analysis. Proc Natl Acad Sci USA 1988; 85: 2444-8.
16. Thompson JD, Higgins DG, Gibson TJ. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22: 4673-80.
17. Gojobori T, Ishii K, Nei M. Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J Mol Evol 1982; 18: 414-23.
18. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406-25.
19. Kimura M. The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press, 1983; 65-97.
20. Stuyver L, De Gendt S, Van Geyt C et al. A new genotype of hepatitis B virus: Complete genome and phylogenetic relatedness. J Gen Virol 2000; 81: 67-74.
21. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39: 783-91.
22. Kalinina O, Norder H, Magnius LO. Full-length open reading frame of a recombinant hepatitis C virus strain from St Petersburg: Proposed mechanism for its formation. J Gen Virol 2004; 85: 1853-7.
23. Kuiken C, Yusin K, Boykin L, Richardson R. The Los Alamos hepatitis C sequence database. Bioinformatics 2005; 21: 379-84.
24. Combet C, Penin F, Geourjon C, Deleage G, Hcvdb. Hepatitis C virus sequences database. Appl Bioinformatics 2004; 3: 237-40.