- Course overview
- Search within this course
- Why Ensembl?
- What is Ensembl?
- When to use Ensembl
- How to access Ensembl
- How to search Ensembl
- How to search Ensembl
- How to search Ensembl
- Exploring sources of biological data
- Navigating Ensembl
- Customise Ensembl
- Manage your data
- Export data
- Download data with BioMart
- Bulk download genome-wide data files with FTP
- Ensembl tools
- Summary
- Guided examples of using Ensembl
- Exercises
- Your feedback
- Get help and support on Ensembl
- Acknowledgements
- Learn more
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Summary
- Why Ensembl? Ensembl aims to organise the vast amount of information in biological databases, and provide one point of access.
- What is Ensembl? Ensembl provides a browser and underlying databases for annotation of vertebrate and non vertebrate genomes. Ensembl genes are based on mainly cDNA and protein evidence in scientific databases. The Ensembl annotation pipeline is combined with Havana manual annotation for major species. Human and mouse gene sets also include the CCDS set. Comparative analyses, sequence variation and regulatory features are all included in Ensembl.
- Where do the data come from? The gene sets come from analyses described above. Whole genome alignments and homology are provided by comparative genomics analyses by the Ensembl team. Variants from dbSNP, COSMIC and other projects are included. Finally, the regulatory features result from Ensembl analyses of data from ENCODE and different FAANG projects.
- How do you access Ensembl? You can access the Ensembl browser through the EBI homepage or by going directly to Ensembl. The database is directly accessible through MySQL queries, or using our REST API and Perl API.
- How can you search Ensembl? You can search the Ensembl browser with gene names, symbols, IDs, genomic regions, variations, descriptions and even diseases or phenotypes.
- How is the data presented in Ensembl? Ensembl presents data in different ways. The information in Ensembl is split into separate tabs. The gene, transcript, location, variation and regulation tabs centre the information on a particular gene, transcript, location, and so on. Each tab has specific displays that you can access from the left-hand menus.
- How do I explore genomes with Ensembl? You can explore a region on a genome, a gene or a splice variant using the location, gene and transcript tabs. The left-hand menu on each tab leads you to more specific views.
- How do I download data? Ensembl data (sequences and alignments) can be exported using the ‘Export data‘ link on the gene, location and transcript tab, BioMart, or the FTP site.