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About


INTRODUCTION

The development of the European Hepatitis C Virus database (euHCVdb) started in 1999 as the French HCV Database (HCVDB, 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.

BOARD

The members of the scientific board of euHCVdb are:

FUNDS

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).

CITATION

TEAM

The euHCVdb is developed at CRCL).

The development team involved:

Name Function Time in project Role in project
Dr C. Combet CR2-CNRS Partial time euHCVdb development coordinator
Dr C. Geourjon IR2-CNRS Partial time Protein 3D atomic models building programs
Dr E. Bettler MC-Univ. Lyon 1 Partial time 3D atomic models analysis tools
C. Charavay HepCVax staff (09/2004-08/2005) Full time Database modelling and entry annotation
D. Crisan HepCVax staff (09/2004-08/2005) Full time Database parsing, SQL queries and query interface
D. Grando VIRGIL staff (03/2005-06/2006) Full time Website and applets, Number tool
J. Lopez VIRGIL staff (01/2006-12/2007) Full time Database and website management, tools
N. Garnier PhD Student Partial time Protein 3D atomic models database managment system and WWW viewing interface
A. Dehne-Garcia Lab's temporary staff Partial time Protein 3D atomic models database scheme

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