The Ensembl Automatic Gene Annotation System

  1. Val Curwen1,
  2. Eduardo Eyras1,
  3. T. Daniel Andrews1,
  4. Laura Clarke1,
  5. Emmanuel Mongin2,
  6. Steven M.J. Searle1, and
  7. Michele Clamp3,4
  1. 1 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
  2. 2 EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
  3. 3 The Broad Institute, Cambridge, Massachusetts 02141, USA

Abstract

As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, and EST sequences. The gene-building system rests on top of the core Ensembl (MySQL) database schema and Perl Application Programming Interface (API), and the data generated are accessible through the Ensembl genome browser (http://www.ensembl.org). To date, the Ensembl predicted gene sets are available for the A. gambiae, C. briggsae, zebrafish, mouse, rat, and human genomes and have been heavily relied upon in the publication of the human, mouse, rat, and A. gambiae genome sequence analysis. Here we describe in detail the gene-building system and the algorithms involved. All code and data are freely available from http://www.ensembl.org.

Footnotes

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1858004.

  • ↵4 Corresponding author. E-MAIL mclamp{at}broad.mit.edu; FAX (617) 258-0903.

    • Accepted January 28, 2004.
    • Received August 8, 2003.
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  1. doi: 10.1101/gr.1858004 Genome Res. 14: 942-950 Cold Spring Harbor Laboratory Press

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