WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in
Guilhem Sempéré1, Katayoun Moazami-Goudarzi2, André Eggen3
1CIRAD, UMR INTERTRYP, F34398, Montpellier, France. guilhem.sempere@cirad.fr.
BMC Genomics
|November 18, 2015
Summary
WIDDE is a new database for exploring cattle genetic diversity using SNP data. It helps manage and analyze large datasets, aiding researchers in understanding bovine biodiversity.
Area of Science:
- Genomics
- Bioinformatics
- Population Genetics
Background:
- Next-generation sequencing generates vast genetic data, posing storage and analysis challenges.
- Efficient management of dense genotyping datasets, especially for cattle, is crucial but difficult.
Purpose of the Study:
- To develop a user-friendly database for managing and exploring cattle genetic diversity.
- To provide a platform for analyzing single nucleotide polymorphism (SNP) data across various cattle populations.
Main Methods:
- Developed WIDDE (Web-Interfaced Next Generation Database), a versatile tool for various species and marker types.
- Created a cattle-specific version with over 750,000 SNPs across 129 populations and 7 outgroup species.
- Implemented data filtering, export options, principal component analysis, and user data integration.
Main Results:
- WIDDE offers a comprehensive dataset for global cattle genetic diversity.
- Users can analyze their own data alongside WIDDE's extensive cattle genetic information.
- The database facilitates population assignment and ancestry estimation for user samples.
Conclusions:
- The cattle WIDDE database is the first of its kind for SNP genotyping data, valuable for bovine biodiversity research.
- WIDDE's generic design allows for future expansion to other species and marker types.
- The database structure supports easy integration of new tools and data formats for enhanced genetic diversity exploration.
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