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HCVDB: hepatitis C virus sequences database

Christophe Combet1, François Penin, Christophe Geourjon

  • 1Institut de Biologie et Chimie des Protéines, UMR 5086, CNRS/UCBL, IFR128 Biosciences Lyon-Gerland, 7 passage du Vercors, 69367 Lyon Cedex 07, France.

Applied Bioinformatics
|February 11, 2005
PubMed

Insights

Hepatitis C virus (HCV) researchers can now access HCVDB, a specialized database simplifying the retrieval, annotation, and analysis of over 30,000 HCV sequences. This automated database enhances data consistency and integrates analysis tools for improved research.

Area of Science:

  • Bioinformatics
  • Virology
  • Genomics

Background:

  • Over 30,000 hepatitis C virus (HCV) sequences are available in generalist databases.
  • Retrieval, annotation, and analysis of these HCV sequences present significant challenges for researchers.
  • Existing databases lack specialized tools for efficient HCV data management.

Purpose of the Study:

  • To develop a specialized, computer-annotated database for hepatitis C virus (HCV) sequences.
  • To address the difficulties in retrieving, annotating, and analyzing large volumes of HCV sequence data.
  • To provide HCV researchers with improved tools for sequence analysis and data management.

Main Methods:

  • Developed HCVDB, a specialized database of computer-annotated HCV sequences.
  • Automated monthly rebuilding of HCVDB from the EMBL database.
  • Integrated HCVDB with sequence and structure analysis tools and the SRS (LION bioscience) keyword query system.

Main Results:

  • HCVDB provides key data including genotype, genomic region, protein functions, and 3D structures for HCV sequences.
  • Ensured consistency of annotations, enabling reliable keyword queries.
  • Facilitated extraction of specific sequence subsets and analysis using integrated bioinformatics programs.

Conclusions:

  • HCVDB offers a valuable resource for hepatitis C virus (HCV) researchers by streamlining data access and analysis.
  • The specialized database improves the efficiency and reliability of HCV sequence research.
  • HCVDB enhances the capabilities for analyzing large-scale viral sequence data.
Abstract

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