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Open Access Highly Accessed Correspondence

Touring Ensembl: A practical guide to genome browsing

Giulietta M Spudich and Xosé M Fernández-Suárez*

Author Affiliations

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SD, UK

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BMC Genomics 2010, 11:295  doi:10.1186/1471-2164-11-295

Published: 11 May 2010

Abstract

The number of databases in molecular biological fields has rapidly increased to provide a large-scale resource. Though valuable information is available, data can be difficult to access, compare and integrate due to different formats and presentations of web interfaces. This paper offers a practical guide to the integration of gene, comparative genomic, and functional genomics data using the Ensembl website at http://www.ensembl.org webcite.

The Ensembl genome browser and underlying databases focus on chordate organisms. More species such as plants and microorganisms can be investigated using our sister browser at http://www.ensemblgenomes.org webcite.

In this study, four examples are used that sample many pages and features of the Ensembl browser. We focus on comparative studies across over 50 mostly chordate organisms, variations linked to disease, functional genomics, and access of external information housed in databases outside the Ensembl project. Researchers will learn how to go beyond simply exporting one gene sequence, and explore how a genome browser can integrate data from various sources and databases to build a full and comprehensive biological picture.