PRABI
Rhone-Alpes Bioinformatics Center


PRABI : IBCP

euHCVdb

European Hepatitis C Virus database (euHCVdb)

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). 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.

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