The Ensembl gene annotation system.

TitleThe Ensembl gene annotation system.
Publication TypeJournal Article
Year of Publication2016
AuthorsAken, BL, Ayling, S, Barrell, D, Clarke, L, Curwen, V, Fairley, S, Banet, JFernandez, Billis, K, Girón, CGarcía, Hourlier, T, Howe, K, Kähäri, A, Kokocinski, F, Martin, FJ, Murphy, DN, Nag, R, Ruffier, M, Schuster, M, Y Tang, A, Vogel, J-H, White, S, Zadissa, A, Flicek, P, Searle, SMJ
JournalDatabase (Oxford)
Volume2016
Date Published2016
ISSN1758-0463
KeywordsAnimals, Databases, Nucleic Acid, Databases, Protein, Humans, Internet, Mice, Molecular Sequence Annotation
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.

DOI10.1093/database/baw093
Alternate JournalDatabase (Oxford)
PubMed ID27337980
PubMed Central IDPMC4919035
Grant ListWT095908 / WT_ / Wellcome Trust / United Kingdom
BB/I025506/1 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/K009524/1 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
WT098051 / WT_ / Wellcome Trust / United Kingdom
BB/I025360/1 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
U54 HG004555 / HG / NHGRI NIH HHS / United States
BB/I025360/2 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/M011615/1 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/E011640/1 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
U41 HG007234 / HG / NHGRI NIH HHS / United States
R01 HD074078 / HD / NICHD NIH HHS / United States
BBS/B/13446 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/M018458/1 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
BBS/B/13470 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/M011461/1 / BB_ / Biotechnology and Biological Sciences Research Council / United Kingdom

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