HBVdb: A knowledge database for Hepatitis B Virus

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Hayer, Juliette ^a   Jadeau, Fanny ^a   Deléage, Gilbert ^a   Kay, Alan ^a   Zoulim, Fabien ^a,b   Combet, Christophe ^a  

^a UNIVERSITÉ LYON 1   (France)

^b HOSPICES CIVILS DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA;

ANTIVIRAL RESISTANCE; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; GENE IDENTIFICATION; GENE STRUCTURE; GENETIC VARIABILITY; GENOTYPING TECHNIQUE; HEPATITIS B VIRUS; KNOWLEDGE BASE; NONHUMAN; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; VIRUS ENVELOPE; VIRUS GENOME; VIRUS RESISTANCE; WEB BROWSER;

DATABASES, GENETIC; DRUG RESISTANCE, VIRAL; GENETIC VARIATION; GENOME, VIRAL; GENOTYPING TECHNIQUES; HEPATITIS B VIRUS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; USER-COMPUTER INTERFACE; VIRAL PROTEINS;

DNA VIRUSES; HEPATITIS B VIRUS;

EID: 84876559113     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1022     Document Type: Article

References (39)

1. Nguyen, D.H., Ludgate, L. and Hu, J. (2008) Hepatitis B virus-cell interactions and pathogenesis. J. Cell. Physiol., 216, 289-294.
2. Zoulim, F. and Locarnini, S. (2009) Hepatitis B virus resistance to nucleos(t)ide analogues. Gastroenterology, 137, 1593-608.e1-2.
3. European Association For The Study Of The Liver. (2009) EASL Clinical Practice Guidelines: management of chronic hepatitis B. J. Hepatol., 50, 227-242.
4. Nassal, M. (2008) Hepatitis B viruses: reverse transcription a different way. Virus Res., 134, 235-249.
5. Bruss, V. (2004) Envelopment of the Hepatitis B Virus nucleocapsid. Virus Res., 106, 199-209.
6. Wynne, S.A., Crowther, R.A. and Leslie, A.G.W. (1999) The crystal structure of the human Hepatitis B Virus capsid. Mol. Cell, 3, 771-780.
7. Glebe, D. and Urban, S. (2007) Viral and cellular determinants involved in hepadnaviral entry. World J. Gastroenterol., 13, 22-38.
8. Benhenda, S., Cougot, D., Buendia, M.-A. and Neuveut, C. (2009) Chapter 4 Hepatitis B Virus X Protein: molecular functions and its role in virus life cycle and pathogenesis. In: Woude, G.F.V. and Klein, G. (eds), Advances in Cancer Research. Academic Press, Vol. 103, pp. 75-109.
9. Bouchard, M.J. and Schneider, R.J. (2004) The enigmatic X gene of hepatitis B virus. J. Virol., 78, 12725-12734.
10. Beck, J. and Nassal, M. (2007) Hepatitis B virus replication. World J Gastroenterol, 13, 48-64.
11. Bartholomeusz, A., Tehan, B.G. and Chalmers, D.K. (2004) Comparisons of the HBV and HIV polymerase, and antiviral resistance mutations. Antivir. Ther., 9, 149-160.
12. Schaefer, S. (2007) Hepatitis B Virus taxonomy and Hepatitis B Virus genotypes. World J. Gastroenterol., 13, 14-21.
13. Norder, H., Couroucé, A.M., Coursaget, P., Echevarria, J.M., Lee, S.D., Mushahwar, I.K., Robertson, B.H., Locarnini, S. and Magnius, L.O. (2004) Genetic diversity of Hepatitis B Virus strains derived worldwide: genotypes, subgenotypes, and HBsAg subtypes. Intervirology, 47, 289-309.
14. Simmonds, P. and Midgley, S. (2005) Recombination in the genesis and evolution of Hepatitis B Virus genotypes. J. Virol., 79, 15467-15476.
15. Kay, A. and Zoulim, F. (2007) Hepatitis B Virus genetic variability and evolution. Virus Res., 127, 164-176.
16. Araujo, N.M., Waizbort, R. and Kay, A. (2011) Hepatitis B Virus infection from an evolutionary point of view: how viral, host, and environmental factors shape genotypes and subgenotypes. Infect. Genet. Evol., 11, 1199-1207.
17. Gnaneshan, S., Ijaz, S., Moran, J., Ramsay, M. and Green, J. (2007) HepSEQ: International Public Health Repository for hepatitis B. Nucleic Acids Res., 35, D367-D370.
18. Shin-I, T., Tanaka, Y., Tateno, Y. and Mizokami, M. (2008) Development and public release of a comprehensive hepatitis virus database. Hepatol. Res., 38, 234-243.
19. Panjaworayan, N., Roessner, S.K., Firth, A.E. and Brown, C.M. (2007) HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in Hepatitis B Virus sequences. Virol. J., 4, 136.
20. Alcantara, L.C., Cassol, S., Libin, P., Deforche, K., Pybus, O.G., Van Ranst, M., Galvão-Castro, B., Vandamme, A.M. and de Oliveira, T. (2009) A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res., 37, W634-W642.
21. Schultz, A.K., Bulla, I., Abdou-Chekaraou, M., Gordien, E., Morgenstern, B., Zoaulim, F., Deny, P. and Stanke, M. (2012) jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. Nucleic Acids Res., 40, W193-W198.
22. Rozanov, M., Plikat, U., Chappey, C., Kochergin, A. and Tatusova, T. (2004) A web-based genotyping resource for viral sequences. Nucleic Acids Res., 32, W654-W659.
23. Rhee, S.Y., Margeridon-Thermet, S., Nguyen, M.H., Liu, T.F., Kagan, R.M., Beggel, B., Verheyen, J., Kaiser, R. and Shafer, R.W. (2010) Hepatitis B Virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery. Antiviral Res., 88, 269-275.
24. Yuen, L.K., Ayres, A., Littlejohn, M., Colledge, D., Edgely, A., Maskill, W.J., Locarnini, S.A. and Bartholomeusz, A. (2007) SeqHepB: a sequence analysis program and relational database system for chronic hepatitis B. Antiviral Res., 75, 64-74.
25. Karsch-Mizrachi, I., Nakamura, Y. and Cochrane, G. (2012). International Nucleotide Sequence Database Collaboration. (2012) The International Nucleotide Sequence Database collaboration. Nucleic Acids Res., 40, D33-D37.
26. Leinonen, R., Akhtar, R., Birney, E., Bower, L., Cerdeno-Tárraga, A., Cheng, Y., Cleland, I., Faruque, N., Goodgame, N., Gibson, R. et al. (2011) The European nucleotide archive. Nucleic Acids Res., 39, D28-D31.
27. Ono, Y., Onda, H., Sasada, R., Igarashi, K., Sugino, Y. and Nishioka, K. (1983) The complete nucleotide sequences of the cloned Hepatitis B Virus DNA; subtype adr and adw. Nucleic Acids Res., 11, 1747-1757.
28. Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
29. Kramvis, A., Arakawa, K., Yu, M.C., Nogueira, R., Stram, D.O. and Kew, M.C. (2008) Relationship of serological subtype, basic core promoter and precore mutations to genotypes/subgenotypes of hepatitis B virus. J. Med. Virol., 80, 27-46.
30. de Oliveira, T., Deforche, K., Cassol, S., Salminen, M., Paraskevis, D., Seebregts, C., Snoeck, J., van Rensburg, E.J., Wensing, A.M., Vijver, D.A. et al. (2005) An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics, 21, 3797-3800.
31. European Association for the Study of the Liver. (2012) EASL Clinical Practice Guidelines: management of chronic Hepatitis B Virus infection. J. Hepatol., 57, 167-185.
32. Stuyver, L.J., Locarnini, S.A., Lok, A., Richman, D.D., Carman, W.F., Dienstag, J.L. and Schinazi, R.F. (2001) Nomenclature for antiviral-resistant human Hepatitis B Virus mutations in the polymerase region. Hepatology, 33, 751-757.
33. Locarnini, S.A. and Yuen, L. (2010) Molecular genesis of drug-resistant and vaccine-escape HBV mutants. Antivir. Ther., 15, 451-461.
34. Combet, C., Garnier, N., Charavay, C., Grando, D., Crisan, D., Lopez, J., Dehne-Garcia, A., Geourjon, C., Bettler, E., Hulo, C. et al. (2007) euHCVdb: the European hepatitis C virus database. Nucleic Acids Res., 35, D363-D366.
35. UniProt Consortium. (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res., 39, D214-D219.
36. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
37. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
38. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
39. Combet, C., Blanchet, C., Geourjon, C. and Deleage, G. (2000) NPS@: network protein sequence analysis. Trends Biochem. Sci., 25, 147.