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The Ensembl automatic gene annotation system.

Val Curwen1, Eduardo Eyras, T Daniel Andrews

  • 1The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Genome Research
|May 5, 2004
PubMed
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The Ensembl gene-building system provides automated annotation for eukaryotic genomes using sequence evidence. This system facilitates rapid access to crucial genomic information for multiple species.

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Increasing genome sequencing necessitates automated annotation for timely data access.
  • Automated gene annotation is crucial for understanding genomic information.

Purpose of the Study:

  • To describe the Ensembl gene-building system for automated eukaryotic genome annotation.
  • To detail the algorithms and processes involved in the Ensembl gene-building system.

Main Methods:

  • Utilizes a gene-building system built on Ensembl's core MySQL database schema and Perl API.
  • Annotates genes using evidence from known protein, cDNA, and expressed sequence tag (EST) sequences.
  • Data is accessible via the Ensembl genome browser.

Main Results:

  • Ensembl predicted gene sets are available for multiple eukaryotic genomes, including human, mouse, rat, zebrafish, A. gambiae, and C. briggsae.

Related Experiment Videos

  • The system has been instrumental in the analysis of several published genome sequences.
  • The gene-building system and its algorithms are described in detail.

    • Conclusions:

    • The Ensembl gene-building system offers an efficient method for automated eukaryotic genome annotation.
    • Freely available code and data promote widespread use and further development in genomics research.