title: The Ensembl automatic gene annotation system.
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.
authors.affiliation: The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Val
authors.initials: V
authors.lastname: Curwen
authors.forename: Eduardo
authors.initials: E
authors.lastname: Eyras
authors.forename: T Daniel
authors.initials: TD
authors.lastname: Andrews
authors.forename: Laura
authors.initials: L
authors.lastname: Clarke
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Mongin
authors.forename: Steven M J
authors.initials: SM
authors.lastname: Searle
authors.forename: Michele
authors.initials: M
authors.lastname: Clamp
mesh_terms: D000818:Animals; D000852:Anopheles / Q000235:genetics; D001331:Automation; D002107:Caenorhabditis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics; D018509:DNA, Helminth / Q000235:genetics; D020224:Expressed Sequence Tags; D018628:Gene Dosage; D005796:Genes / Q000502:physiology*; D017238:Genes, Helminth / Q000502:physiology; D017344:Genes, Insect / Q000502:physiology; D016678:Genome; D015894:Genome, Human; D015801:Helminth Proteins / Q000235:genetics; D006801:Humans; D019476:Insect Proteins / Q000235:genetics; D051379:Mice; D011237:Predictive Value of Tests; D011506:Proteins / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics; D051381:Rats; D016415:Sequence Alignment / Q000379:methods; D017386:Sequence Homology, Amino Acid; D012984:Software; D020080:Tandem Repeat Sequences / Q000235:genetics; D020506:Untranslated Regions / Q000235:genetics
chemical_list: D018509:DNA, Helminth; D015801:Helminth Proteins; D019476:Insect Proteins; D011506:Proteins; D020506:Untranslated Regions; D004247:DNA