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. 2010 May 11:11:238.
doi: 10.1186/1471-2105-11-238.

A database and API for variation, dense genotyping and resequencing data

Daniel Rios  1 , William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham
Affiliations

A database and API for variation, dense genotyping and resequencing data

Daniel Rios et al. BMC Bioinformatics. .

Abstract

Background: Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and manipulation of such data necessitating the redesign of existing genome-wide bioinformatics resources.

Results: Ensembl has created a database and software library to support data storage, analysis and access to the existing and emerging variation data from large mammalian and vertebrate genomes. These tools scale to thousands of individual genome sequences and are integrated into the Ensembl infrastructure for genome annotation and visualisation. The database and software system is easily expanded to integrate both public and non-public data sources in the context of an Ensembl software installation and is already being used outside of the Ensembl project in a number of database and application environments.

Conclusions: Ensembl's powerful, flexible and open source infrastructure for the management of variation, genotyping and resequencing data is freely available at http://www.ensembl.org.

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Figures

Figure 1
Figure 1
Simplified Database Schema. A simplified version of the Ensembl variation database schema. Sequence variants are stored in the variation table shown in the top centre of the figure. A sequence variant is defined as having a source, flanking sequence and at least one allele. Structural variants have their own table. Connections to the Ensembl core database for sequencing information and genome annotations are highlighted. The full database schema is provided as a supplemental file and available at http://www.ensembl.org/info/docs/api/variation/variation_schema.html.
Figure 2
Figure 2
Using the API to access variation and sequence. This example describes how to use the registry and the API to connect to an Ensembl database and access and analyse variation from a specific region of the genome in a given individual sequence.
Figure 3
Figure 3
Linkage Disequilibrium Plot. The pattern of linkage disequilibrium (LD) in the HapMap CEU population for a 20 kb region of the BRCA2 gene. The displayed values for r2 and D' are calculated on the fly by the variation API, which calls a dedicated C function after the necessary data is extracted from the database.
See this image and copyright information in PMC

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