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Briefings in Functional Genomics and Proteomics Advance Access originally published online on October 29, 2007
Briefings in Functional Genomics and Proteomics 2007 6(3):202-219; doi:10.1093/bfgp/elm025
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© Oxford University Press, 2007, All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Special Issue Papers

Genome browsing with Ensembl: a practical overview

Giulietta Spudich, Xosé M. Fernández-Suárez and Ewan Birney

Corresponding author. Ewan Birney, EMBL Outstation – EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. Tel: +44(0)1223 494992; Fax: +44(0)1223 494468; E-mail: birney{at}ebi.ac.uk

A wealth of gene information is accruing in public databases. Genome browsers such as Ensembl are needed to organize and depict this information in the context of the genome. Ensembl provides an open source gene set based on experimental evidence for over 30 species, the majority of which are vertebrates. Genes and annotation are accessible through the Ensembl browser (http://www.ensembl.org), and through direct queries of its databases using the Perl API (Application Programme Interface), MySQL or BioMart.

Keywords: Ensembl, genome browser, annotation, data mining, gene prediction, comparative genomics


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