The development of the European Hepatitis C Virus database (euHCVdb) started in 1999 as the French HCV Database
Combet et al.,2004). The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural
biology of HCV (Penin et al., 2004).
In order to make the existing HCV databases as complementary as possible, the current developments are coordinated with the other databases (Japan and Los Alamos) as part
of an international collaborative effort (Kuiken et al., 2006).
It is monthly updated from the EMBL Nucleotide sequence database and maintained in a relational database
management system (PostgreSQL). Programs for parsing the EMBL database flat files, annotating HCV entries, filling up and querying the
database used SQL and Java programming languages. Great efforts have been made to develop a fully automatic annotation procedure thanks to a
reference set of HCV complete annotated well-characterized genomes of various genotypes.
This automatic procedure ensures standardisation of nomenclature for all entries and provides genomic regions/proteins present in the entry,
bibliographic reference, genotype, interesting sites (e.g. HVR1) or domains (e.g. NS3 helicase), source of the sequence (e.g. isolate) and
structural data that are available as protein 3D models.
The members of the scientific board of euHCVdb are:
- Pr Amos Bairoch (Swiss Institue for Bioinformatics, Switzerland)
- Pr Dr Ralf Bartenschlager (University of Heidelberg, Germany)
- Dr Helmut Diepolder (University of Munich, Germany)
- Pr Darius Moradpour (Centre Hospitalier Universitaire Vaudois, Switzerland)
- Pr Jean-Michel Pawlotsky (Henri Mondor University Hospital, France)
- Dr Francois Penin (Institut de Biologie et Chimie des Proteines, France)
- Dr Charles Rice (Rockfeller Univeristy, USA)
- Pr Christian Trepo (Lyon University Hospital, France)
The euHCVdb is funded as part of the HepCVax cluster
(EC grant QLK2-CT-2002-01329)
and viRgil network of excellence
(EC grant LSHM-CT-2004-503359).
- HCV databases: Hepatitis C databases, principles and utility to researchers.
Kuiken C, Mizokami M, Deléage G, Yusim K, Penin F, Shin-I T, Charavay C, Tao
N, Crisan D, Grando D, Dalwani A, Geourjon C, Agrawal A, Combet C.
Hepatology, 2006, 43:1157-1165.
- This database: euHCVdb: the European hepatitis C virus database.
Combet C., Garnier N., Charavay C., Grando D., Crisan D., Lopez J., Dehne-Garcia A., Geourjon C., Bettler E., Hulo C., Mercier PL., Bartenschlager R., Diepolder H., Moradpour D., Pawlotsky J.M., Rice C.M., Trepo C., Penin F. and Deléage G.
Nucleic Acids Res, 2007, 35:D363-D366.
- Original french database: HCVDB: Hepatitis C Virus Sequences Database.
Combet C., Penin F., Geourjon C. and Deléage G.
Appl. Bioinformatics, 2004, 3:237-240.
The euHCVdb is developed at CRCL).
The development team involved:
||Time in project
||Role in project
|Dr C. Combet
||euHCVdb development coordinator
|Dr C. Geourjon
||Protein 3D atomic models building programs
|Dr E. Bettler
||MC-Univ. Lyon 1
||3D atomic models analysis tools
||HepCVax staff (09/2004-08/2005)
||Database modelling and entry annotation
||HepCVax staff (09/2004-08/2005)
||Database parsing, SQL queries and query interface
||VIRGIL staff (03/2005-06/2006)
||Website and applets, Number tool
||VIRGIL staff (01/2006-12/2007)
||Database and website management, tools
||Protein 3D atomic models database managment system and WWW viewing interface
||Lab's temporary staff
||Protein 3D atomic models database scheme
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