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Database (Oxford). 2016 Jun 23;2016. pii: baw093. doi: 10.1093/database/baw093. Print 2016.

The Ensembl gene annotation system.

Author information

1
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.
2
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.
3
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.
4
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.
5
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
6
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Pfizer Inc, 10646 Science Center Dr, San Diego, CA 92121, USA.
7
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.
8
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.
9
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.
10
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.
11
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.
12
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK bronwen.aken@ebi.ac.uk smjsearle@yahoo.co.uk.

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.

PMID:
27337980
PMCID:
PMC4919035
DOI:
10.1093/database/baw093
[Indexed for MEDLINE]
Free PMC Article

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