WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle

• Published in: BMC Genomics 2015, Vol.16 (934)
• Main Authors: Sempñrñ, Guilhem, Moazami-Goudarzi, Katayoun, Eggen, Andrñ, Laloë, Denis, Gautier, Mathieu, Flori, Laurence
• Format: Report
• Language: English
• Subjects: Analysis; Biological diversity; Single nucleotide polymorphisms
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-015-2181-1

Background The advent and democratization of next generation sequencing and genotyping technologies lead to a huge amount of data for the characterization of population genetic diversity in model and non model-species. However, efficient storage, management, cross-analyzing and exploration of such dense genotyping datasets remain challenging. This is particularly true for the bovine species where many SNP datasets have been generated in various cattle populations with different genotyping tools. Description We developed WIDDE, a Web-Interfaced Next Generation Database that stands as a generic tool applicable to a wide range of species and marker types ( Conclusion The cattle version of WIDDE represents to our knowledge the first database dedicated to cattle biodiversity and SNP genotyping data that will be very useful for researchers interested in this field. As a generic tool applicable to a wide range of marker types, WIDDE is overall intended to the genetic diversity exploration of any species and will be extended to other species shortly. The structure makes it easy to include additional output formats and new tools dedicated to genetic diversity exploration. Keywords: Polymorphism, SNP, Genetic diversity, Principal component analysis, NoSQL, Allele sharing distance, Population assignment, Cattle