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

BMC Bioinformatics

Software

Paul Flicek¹  Fiona Cunningham¹  Arne Stabenau¹  Daniel Rios¹  William M McLaren¹  Yuan Chen¹  Ewan Birney¹ 

[1] European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK;

关键词: Variation Data;    Application Program Interface;    UCSC Genome Browser;    Variation Object;    Variation Database;   

DOI  :  10.1186/1471-2105-11-238

 received in 2009-09-23, accepted in 2010-05-11,  发布年份 2010

来源: Springer

【 摘 要 】

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

【 授权许可】

Unknown   
© Rios et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.