title: The Ensembl gene annotation system.
abstract: The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK bronwen.aken@ebi.ac.uk smjsearle@yahoo.co.uk.
authors.forename: Bronwen L
authors.initials: BL
authors.lastname: Aken
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Present addresses: The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Sarah
authors.initials: S
authors.lastname: Ayling
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Eagle Genomics Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK.
authors.forename: Daniel
authors.initials: D
authors.lastname: Barrell
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Laura
authors.initials: L
authors.lastname: Clarke
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Valery
authors.initials: V
authors.lastname: Curwen
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Susan
authors.initials: S
authors.lastname: Fairley
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Pfizer Inc, 10646 Science Center Dr, San Diego, CA 92121, USA.
authors.forename: Julio
authors.initials: J
authors.lastname: Fernandez Banet
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Billis
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Carlos
authors.initials: C
authors.lastname: García Girón
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Thibaut
authors.initials: T
authors.lastname: Hourlier
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Kevin
authors.initials: K
authors.lastname: Howe
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Institutionen för cell-och molekylärbiologi, Uppsala University, Husargatan 3, Uppsala 752 37, Sweden.
authors.forename: Andreas
authors.initials: A
authors.lastname: Kähäri
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Felix
authors.initials: F
authors.lastname: Kokocinski
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Fergal J
authors.initials: FJ
authors.lastname: Martin
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Murphy
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Rishi
authors.initials: R
authors.lastname: Nag
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Magali
authors.initials: M
authors.lastname: Ruffier
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna a-1090, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Schuster
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Y Amy
authors.initials: YA
authors.lastname: Tang
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.
authors.forename: Jan-Hinnerk
authors.initials: JH
authors.lastname: Vogel
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Simon
authors.initials: S
authors.lastname: White
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Amonida
authors.initials: A
authors.lastname: Zadissa
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK bronwen.aken@ebi.ac.uk smjsearle@yahoo.co.uk.
authors.forename: Stephen M J
authors.initials: SM
authors.lastname: Searle
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D051379:Mice; D058977:Molecular Sequence Annotation / Q000379:methods*