The Ensembl gene annotation system
Database2016Vol. 2016, pp. baw093–baw093
Citations Over TimeTop 1% of 2016 papers
Bronwen Aken, Sarah Ayling, Daniel Barrell, Laura Clarke, V. Curwen, Susan Fairley, Julio Fernandez-Banet, Konstantinos Billis, Carlos García Girón, Thibaut Hourlier, Kevin Howe, Andreas Kähäri, Felix Kokocinski, Fergal J. Martin, Daniel N. Murphy, Rishi Nag, Magali Ruffier, Michael Schuster, Amy Tang, Jan-Hinnerk Vogel, Simon White, Amonida Zadissa, Paul Flicek, Stephen M. J. Searle
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.
Related Papers
- → GENCODE: reference annotation for the human and mouse genomes in 2023(2022)613 cited
- → The UCSC Known Genes(2006)518 cited
- → A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification(2015)142 cited
- → sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters(2009)38 cited
- → Impact of gene annotation choice on the quantification of RNA-seq data(2022)22 cited