Abstract
Abstract: To date, more than 30 000 hepatitis C virus (HCV) sequences have been deposited in the generalist databases DNA Data Bank of Japan (DDBJ), EMBL Nucleotide Sequence Database (EMBL) and GenBank®. The main difficulties with HCV sequences in these databases are their retrieval, annotation and analyses. To help HCV researchers face the increasing needs of HCV sequence analyses, we developed a specialised database of computer-annotated HCV sequences, called HCVDB. HCVDB is re-built every month from an up-to-date EMBL database by an automated process. HCVDB provides key data about the HCV sequences (e.g. genotype, genomic region, protein names and functions, known 3-dimensional structures) and ensures consistency of the annotations, which enables reliable keyword queries. The database is highly integrated with sequence and structure analysis tools and the SRS (LION bioscience) keywords query system. Thus, any user can extract subsets of sequences matching particular criteria or enter their own sequences and analyse them with various bioinformatics programs available on the same server.
Availability: HCVDB is available from http://hepatitis.ibcp.fr
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Acknowledgements
This work was supported by Reséau National Hépatites of ‘Programme national de recherche fondamentale en microbiologie et maladies infectieuses et parasitaires du Ministére de la Recherche’ and the EU contract QLK2-CT-2002-01329. C. Combet received a doctoral fellowship from Agence National de Recherches sur le Sida (ANRS). The authors gratefully acknowledge Christian Bréchot, Jean Dubuisson, Geneviève Inchauspé and Jean-Michel Pawlotsky for stimulating discussions and their support for HCVDB creation. The authors have no conflicts of interest that are directly relevant to the content of this article.
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Combet, C., Penin, F., Geourjon, C. et al. HCVDB. Appl-Bioinformatics 3, 237–240 (2004). https://doi.org/10.2165/00822942-200403040-00005
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DOI: https://doi.org/10.2165/00822942-200403040-00005