The Ensembl gene annotation system

• Published in: Database : the journal of biological databases and curation Vol. 2016; p. baw093
• Main Authors: Aken, Bronwen L., Ayling, Sarah, Barrell, Daniel, Clarke, Laura, Curwen, Valery, Fairley, Susan, Fernandez Banet, Julio, Billis, Konstantinos, García Girón, Carlos, Hourlier, Thibaut, Howe, Kevin, Kähäri, Andreas, Kokocinski, Felix, Martin, Fergal J., Murphy, Daniel N., Nag, Rishi, Ruffier, Magali, Schuster, Michael, Tang, Y. Amy, Vogel, Jan-Hinnerk, White, Simon, Zadissa, Amonida, Flicek, Paul, Searle, Stephen M. J.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 2016
• Subjects: Animals; Database Update; Databases, Nucleic Acid; Databases, Protein; Humans; Internet; Mice; Molecular Sequence Annotation - methods
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/baw093

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.