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LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-box" approach
Ivo F A C Fokkema1, Johan T den Dunnen, Peter E M Taschner
1Center of Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.
Human Mutation
|June 25, 2005
Summary
The Leiden Open (source) Variation Database (LOVD) offers an easy, web-based solution for creating and maintaining gene sequence variation databases. This open-source software facilitates the collection and display of DNA variations, promoting community-driven extensions.
Area of Science:
- Genomics
- Bioinformatics
- Database Development
Background:
- The Human Genome Project necessitates comprehensive databases for human sequence variation.
- Gene-centered, locus-specific databases (LSDBs) are crucial for accessing variation data.
- Existing solutions may lack ease of creation and maintenance.
Purpose of the Study:
- To develop a user-friendly, web-based software for creating and maintaining gene sequence variation databases.
- To provide a platform adhering to Human Genome Variation Society (HGVS) recommendations.
- To encourage community contributions and extensions.
Main Methods:
- Development of the Leiden Open (source) Variation Database (LOVD) software.
- Utilizing open-source technologies: PHP and MySQL.
- Implementing a gene-centered, modular design.
Main Results:
- LOVD software provides an 'LSDB-in-a-Box' solution for easy database creation and maintenance.
- The platform is platform-independent and focuses on DNA sequence variation collection and display.
- LOVD is extendable with clinical data and community-developed scripts.
Conclusions:
- LOVD offers an efficient, open-source solution for managing gene sequence variation data.
- The software promotes standardization and community collaboration in genomic variation studies.
- Free availability and support encourage widespread adoption by researchers and curators.