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VBASE2, an integrative V gene database
Ida Retter1, Hans Helmar Althaus, Richard Münch
1Department of Experimental Immunology, German Research Centre for Biotechnology, Mascheroder Weg 1, D-38124 Braunschweig, Germany.
Nucleic Acids Research
|December 21, 2004
Summary
VBASE2 is a comprehensive database for human and mouse immunoglobulin variable (V) genes. It integrates genomic data and links to other key resources, facilitating V gene research.
Area of Science:
- Immunology
- Bioinformatics
- Genomics
Background:
- Immunoglobulin variable (V) genes are crucial for adaptive immunity.
- Existing databases for V gene sequences are often fragmented.
- Integrating these resources is essential for comprehensive analysis.
Purpose of the Study:
- To present VBASE2, a unified database for human and mouse immunoglobulin V gene sequences.
- To enhance data accessibility and interoperability with existing bioinformatics resources.
- To provide a centralized platform for V gene sequence retrieval and analysis.
Main Methods:
- Integration of germ-line sequences for human and mouse immunoglobulin V genes.
- Linking VBASE2 with the Ensembl Genome Browser for genomic context.
- Establishing cross-references to EMBL, VBASE, IMGT, and Kabat databases.
- Implementing a DAS server for visualization within Ensembl.
- Providing web-based text query and DNAPLOT for sequence similarity search.
Main Results:
- VBASE2 offers a consolidated repository of immunoglobulin V gene sequences.
- Seamless integration with Ensembl Genome Browser allows for genomic visualization.
- Comprehensive cross-referencing enhances data discovery and validation.
- Multiple access methods cater to diverse user needs in V gene research.
Conclusions:
- VBASE2 serves as a valuable, interconnected resource for researchers studying immunoglobulin V genes.
- The database facilitates efficient retrieval and analysis of V gene data.
- Enhanced data integration and accessibility in VBASE2 advance immunological and genomic research.
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