Bioinformatics Advance Access originally published online on September 17, 2004
Bioinformatics 2005 21(3):379-384; doi:10.1093/bioinformatics/bth485
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Bioinformatics vol. 21 issue 3 © Oxford University Press 2005; all rights reserved.
The Los Alamos hepatitis C sequence database
HCV database, Los Alamos National Laboratory Los Alamos, NM, USA
*To whom correspondence should be addressed.
Motivation: The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide.
Results: The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of 
280 visits per day from distinct IP addresses.
Availability: The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org
Contact: hcv-info{at}lanl.gov
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Hughes, S. Gretton, H. Shelton, D. D. Brown, C. J. McCormick, A. G. N. Angus, A. H. Patel, S. Griffin, and M. Harris A Conserved Proline between Domains II and III of Hepatitis C Virus NS5A Influences both RNA Replication and Virus Assembly J. Virol., October 15, 2009; 83(20): 10788 - 10796. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Bruns, K. Steinmetzer, E. Ermantraut, and A. Stallmach Hepatitis C Virus RNA Quantitation in Venous and Capillary Small-Volume Whole-Blood Samples J. Clin. Microbiol., October 1, 2009; 47(10): 3231 - 3240. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Ford, F. A. Matsen, and T. Stadler A Method for Investigating Relative Timing Information on Phylogenetic Trees Syst Biol, June 12, 2009; (2009) syp018v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Hughes, S. Griffin, and M. Harris Domain III of NS5A contributes to both RNA replication and assembly of hepatitis C virus particles J. Gen. Virol., June 1, 2009; 90(6): 1329 - 1334. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Love, O. Brodsky, M. J. Hickey, P. A. Wells, and C. N. Cronin Crystal Structure of a Novel Dimeric Form of NS5A Domain I Protein from Hepatitis C Virus J. Virol., May 1, 2009; 83(9): 4395 - 4403. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. G. Pybus, E. Barnes, R. Taggart, P. Lemey, P. V. Markov, B. Rasachak, B. Syhavong, R. Phetsouvanah, I. Sheridan, I. S. Humphreys, et al. Genetic History of Hepatitis C Virus in East Asia J. Virol., January 15, 2009; 83(2): 1071 - 1082. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Hraber, C. Kuiken, M. Waugh, S. Geer, W. J. Bruno, and T. Leitner Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index J. Gen. Virol., September 1, 2008; 89(9): 2098 - 2107. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. J. Irausquin and A. L. Hughes Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures J. Gen. Virol., August 1, 2008; 89(8): 1921 - 1929. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. J. Harris, M. J. Farquhar, C. J. Mee, C. Davis, G. M. Reynolds, A. Jennings, K. Hu, F. Yuan, H. Deng, S. G. Hubscher, et al. CD81 and Claudin 1 Coreceptor Association: Role in Hepatitis C Virus Entry J. Virol., May 15, 2008; 82(10): 5007 - 5020. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Noppornpanth, Y. Poovorawan, T. X. Lien, S. L. Smits, A. D. M. E. Osterhaus, and B. L. Haagmans Complete genome analysis of hepatitis C virus subtypes 6t and 6u J. Gen. Virol., May 1, 2008; 89(5): 1276 - 1281. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Neumann-Haefelin, D. N. Frick, J. J. Wang, O. G. Pybus, S. Salloum, G. S. Narula, A. Eckart, A. Biezynski, T. Eiermann, P. Klenerman, et al. Analysis of the Evolutionary Forces in an Immunodominant CD8 Epitope in Hepatitis C Virus at a Population Level J. Virol., April 1, 2008; 82(7): 3438 - 3451. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Birin, Z. Gal-Or, I. Elias, and T. Tuller Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion Bioinformatics, March 15, 2008; 24(6): 826 - 832. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. L. Tellinghuisen, K. L. Foss, J. C. Treadaway, and C. M. Rice Identification of Residues Required for RNA Replication in Domains II and III of the Hepatitis C Virus NS5A Protein J. Virol., February 1, 2008; 82(3): 1073 - 1083. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-C. Meunier, R. S. Russell, V. Goossens, S. Priem, H. Walter, E. Depla, A. Union, K. N. Faulk, J. Bukh, S. U. Emerson, et al. Isolation and Characterization of Broadly Neutralizing Human Monoclonal Antibodies to the E1 Glycoprotein of Hepatitis C Virus J. Virol., January 15, 2008; 82(2): 966 - 973. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. L. Murray, C. T. Jones, J. Tassello, and C. M. Rice Alanine Scanning of the Hepatitis C Virus Core Protein Reveals Numerous Residues Essential for Production of Infectious Virus J. Virol., October 1, 2007; 81(19): 10220 - 10231. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C Hourioux, R Patient, A Morin, E Blanchard, A Moreau, S Trassard, B Giraudeau, and P Roingeard The genotype 3-specific hepatitis C virus core protein residue phenylalanine 164 increases steatosis in an in vitro cellular model Gut, September 1, 2007; 56(9): 1302 - 1308. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Schulze zur Wiesch, G. M. Lauer, J. Timm, T. Kuntzen, M. Neukamm, A. Berical, A. M. Jones, B. E. Nolan, S. A. Longworth, V. Kasprowicz, et al. Immunologic evidence for lack of heterologous protection following resolution of HCV in patients with non genotype 1 infection Blood, September 1, 2007; 110(5): 1559 - 1569. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Donlin, N. A. Cannon, E. Yao, J. Li, A. Wahed, M. W. Taylor, S. H. Belle, A. M. Di Bisceglie, R. Aurora, J. E. Tavis, et al. Pretreatment Sequence Diversity Differences in the Full-Length Hepatitis C Virus Open Reading Frame Correlate with Early Response to Therapy J. Virol., August 1, 2007; 81(15): 8211 - 8224. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Neumann-Haefelin, T. Killinger, J. Timm, S. Southwood, D. McKinney, H. E. Blum, and R. Thimme Absence of viral escape within a frequently recognized HLA-A26-restricted CD8+ T-cell epitope targeting the functionally constrained hepatitis C virus NS5A/5B cleavage site J. Gen. Virol., July 1, 2007; 88(7): 1986 - 1991. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Lu, C. Li, Y. Fu, L. Thaikruea, S. Thongswat, N. Maneekarn, C. Apichartpiyakul, H. Hotta, H. Okamoto, D. Netski, et al. Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses J. Gen. Virol., May 1, 2007; 88(5): 1505 - 1518. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. G. Murphy, B. Willems, M. Deschenes, N. Hilzenrat, R. Mousseau, and S. Sabbah Use of Sequence Analysis of the NS5B Region for Routine Genotyping of Hepatitis C Virus with Reference to C/E1 and 5' Untranslated Region Sequences J. Clin. Microbiol., April 1, 2007; 45(4): 1102 - 1112. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Combet, N. Garnier, C. Charavay, D. Grando, D. Crisan, J. Lopez, A. Dehne-Garcia, C. Geourjon, E. Bettler, C. Hulo, et al. euHCVdb: the European hepatitis C virus database Nucleic Acids Res., January 12, 2007; 35(suppl_1): D363 - D366. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Naito, K. Ui-Tei, T. Nishikawa, Y. Takebe, and K. Saigo siVirus: web-based antiviral siRNA design software for highly divergent viral sequences. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W448 - W450. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-F. Cantaloube, S. Laperche, P. Gallian, F. Bouchardeau, X. de Lamballerie, and P. de Micco Analysis of the 5' Noncoding Region versus the NS5b Region in Genotyping Hepatitis C Virus Isolates from Blood Donors in France. J. Clin. Microbiol., June 1, 2006; 44(6): 2051 - 2056. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Laperche, K. Saune, P. Deny, G. Duverlie, S. Alain, M.-L. Chaix, C. Gaudy, F. Lunel, J.-M. Pawlotsky, C. Payan, et al. Unique NS5b Hepatitis C Virus Gene Sequence Consensus Database Is Essential for Standardization of Genotype Determinations in Multicenter Epidemiological Studies J. Clin. Microbiol., February 1, 2006; 44(2): 614 - 616. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Schulze zur Wiesch, G. M. Lauer, C. L. Day, A. Y. Kim, K. Ouchi, J. E. Duncan, A. G. Wurcel, J. Timm, A. M. Jones, B. Mothe, et al. Broad Repertoire of the CD4+ Th Cell Response in Spontaneously Controlled Hepatitis C Virus Infection Includes Dominant and Highly Promiscuous Epitopes J. Immunol., September 15, 2005; 175(6): 3603 - 3613. [Abstract] [Full Text] [PDF]
|
|