Genomics · Database
Ensembl
A centralised genome browser and database providing automated annotation for human and other vertebrate genomes.
What Ensembl is
Ensembl is a scientific genome database project developed at the European Bioinformatics Institute (EMBL-EBI). Started in 1999 to support the Human Genome Project, it addresses the challenge of identifying gene locations, regulatory features, and sequence relationships across entire genomes by automating annotation using computational pipelines rather than relying solely on manual curation.
The platform focuses on vertebrate genomes and key model organisms, holding data on genes, transcripts, sequences, genetic variations, regulatory features, and homology across species. It also integrates specialised tools such as the Variant Effect Predictor and provides access to major reference assemblies including human builds GRCh38 and GRCh37.
Ensembl serves molecular biologists, geneticists, and computational researchers by providing open, centralised access to standardised eukaryotic genome annotations. Researchers can explore genomic architectures interactively, compare orthologous sequences, analyse variations, and extract large-scale datasets for downstream analysis.
How it is organised
Raw sequence data are fed into an automated gene annotation pipeline composed of Perl software modules. This pipeline matches protein sequences to DNA to predict gene structures and locations, writing the outputs to a structured MySQL database backend.
Data are presented through a graphical web browser developed using Perl and the GD graphics library, which visualises genomic alignments as configurable tracks ranging from whole karyotypes to nucleotide and amino acid sequences. Beyond the web interface, data access is facilitated via direct MySQL queries, an FTP server, the BioMart data-mining tool, and programming interfaces including REST and specialised Perl APIs (covering core features, comparative genomics, variation, and functional genomics).
Key facts
- Project start year
- 1999
- Category
- Genomics
- Primary species coverage
- Vertebrates and selected model organisms
- Registered species count
- 271 species (as of 2022)
- Human genome assemblies
- GRCh37 and GRCh38
- Database backend
- MySQL
- Data export and exchange formats
- FASTA, BAM, BED, PSL
- Software interfaces
- Perl API, REST API, BioMart, FTP server, direct SQL
What you can use it for
- Variant effect analysis
- Evaluate the functional consequences of genetic variants such as single-nucleotide polymorphisms, single-nucleotide variants, and copy-number variations using the integrated Variant Effect Predictor.
- Comparative genomics and homology assessment
- Inspect phylogenetic trees and cross-species gene homologues using comparative genomics tracks and the Compara API.
- Genomic region visualisation
- Browse, zoom, and navigate along reference chromosomes to examine gene models, transcripts, regulatory features, and uploaded custom tracks in formats like BAM or BED.
- Bulk data extraction
- Extract tailored datasets of genes, sequences, and cross-references across multiple species using the BioMart data-mining interface or FTP downloads.
Query it here
The research agent queries Ensembl directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.
Strengths and limits
Good at
- Provides programmatic data retrieval through both REST and modular Perl APIs covering core annotations, comparative genomics, variation, and regulatory features.
- Facilitates flexible visual exploration by allowing users to toggle individual annotation tracks and display resolutions from chromosome karyotypes down to base-pair sequences.
- Allows users to overlay custom experimental datasets in common formats such as BAM, BED, and PSL directly onto the reference genome display.
Watch out for
- Coverage within the primary Ensembl project is restricted to eukaryotes, specifically vertebrates and selected model organisms, containing no prokaryotic genomes.
- Querying the public MySQL database directly with SQL requires extensive familiarity with the underlying database schema.
Questions
Can I search Ensembl without writing code?
Yes. The research agent queries Ensembl directly, with no account or API key, and cites the record behind every answer. Ask in plain language — for a gene, a protein, a compound or a study — and it builds the query for you.
Can I reuse data from Ensembl?
No restrictions on data use; EMBL-EBI terms of use. Terms: https://www.ensembl.org/info/about/legal/disclaimer.html
Which human reference genome assemblies are available on Ensembl?
Ensembl supports both the GRCh37 and GRCh38 human genome assemblies.
Can I view my own sequencing or mapping data alongside Ensembl annotations?
Yes. The web interface permits users to upload and view custom external datasets in standard formats such as BAM, BED, or PSL.
How can large volumes of genomic data be downloaded without direct scripting?
Large datasets can be queried and retrieved through the BioMart web interface, or downloaded directly from the public FTP server.
Does Ensembl annotate bacteria or viruses?
The primary Ensembl database contains only eukaryotic genomes and no prokaryotes, although its scope expanded in 2020 to include a dedicated site for the SARS-CoV-2 reference genome, while non-vertebrate groups are handled by the sister project Ensembl Genomes.
Written from Ensembl's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.