Following the recent launch of Google DeepMind’s AlphaGenome Atlas, the Ensembl Variant Effect Predictor (Ensembl VEP) has now integrated AlphaGenome Variant Impact (AVI) scores. This integration enables researchers to easily access AI-generated scores which estimate how likely genetic variants across the whole genome are to be deleterious. These are available to use now for human reference in the new Ensembl and the Ensembl 116 archive.
Continue readingTag: Bioinformatics
Ensembl is moving to our new platform this week
Ensembl is moving to our new platform for genome data and annotation this week. We will begin with the Ensembl Genomes sites and end with the Ensembl 116 site at www.ensembl.org.
The default URL for our new site will be www.ensembl.org. This site offers new scientific opportunities, as genomes and genesets are now available for a diverse array of species from across the tree of life.
Please explore the site and the range of data available, and contact us with your needs, especially regarding new data and working with pangenome data.
There are many new features coming to the new Ensembl, along with the features you have come to love in our legacy sites. If there is a feature you need which is not yet available on the new site, the legacy sites remain available via our archives.
We have a new integrated release on our new site – 2026-07 – which integrates the latest genesets from the Ensembl 116 and Ensembl Genomes 63 releases. Read more.
We also delivered webinars on transition topics, including Educating with Ensembl, the new site, and programmatic access to genome data. Recordings are available.
Thank you for your patience over this transition period, and for joining us as we aim to share more genome data than ever before. We look forward to the insights and discoveries to come.
Feature profile between new and legacy Ensembl – July 2026 update
The new Ensembl site provides broader availability of species and genomes, but as it is in active development, not all the features from the legacy Ensembl (Ensembl 116 and Ensembl Genomes 63) versions are available. Here is a list of features profiled between the versions to help you choose which resource to use. These are valid as of July 2026.
Ensembl sites and data remain available via Ensembl Archives, please use whichever resource meets your needs best.
Continue readingEnsembl 116 and Ensembl Genomes 63 have been released!
Ensembl 116 and Ensembl Genomes 63 are here! Highlights include new pig & cattle assemblies, 26 oat genomes, updated alignments and new Ensembl VEP plugins.
Special Notice – Ensembl Transition
Ensembl 116 and Ensembl Genomes 63 are the final releases on the current Ensembl site and platforms.
All new data from this point will only be available through the new Ensembl site. In the next few months, the ensembl.org site will bring you to the site hosted on beta.ensembl.org.
You will continue to have access to current Ensembl versions via Ensembl Archives, with the latest archives having extended tool support. The Ensembl USEast and Asia mirrors of the current main site will be retired over the transition period this summer.
Continue readingEnsembl MySQL services will be upgraded to MySQL 8 soon
Users of the publicly accessible Ensembl MySQL servers should note that we will soon be upgrading these services from MySQL 5.6 to MySQL 8.
Continue readingExpanded transcript set available in the latest human GRCh38 partial release on the new Ensembl site
In the current Ensembl release (Ensembl 115), the GRCh38 human Ensembl/GENCODE reference annotation was updated to include approximately 121,000 new protein-coding transcripts. This expanded set is based on long-read RNA-seq data processed by the manually supervised automated pipeline TAGENE, which is presented as the source in both browser and files.
The latest partial release for GRCh38 on the new Ensembl (partial release 2026-01-26) includes this new geneset. Some genes and genomic features in this set have several hundred transcripts, such as ZBTB20 (ENSG00000181722) which has 360 transcripts.
Continue readingWhat’s coming in Ensembl release 116 / Ensembl Genomes 63?
Ensembl 116 and Ensembl Genomes 63 are expected in April 2026. Check out what we’re up to, although we can’t guarantee everything listed here will make it into the release.
Special Notice
Ensembl 116 and Ensembl Genomes 63 will be the final releases on the current Ensembl site and platforms.
From the summer of 2026, all new data will only be available through the new Ensembl site. The site, ensembl.org, will redirect to the site currently hosted on beta.ensembl.org.
Continue readingGetting to know us: Disha Lodha (Ensembl Plants & Metazoa)
In our Teamsembl blog series, we sit down with a member of the Ensembl team to talk about their role within the project and get to know them. This month, we had a chat with Disha Lodha, a bioinformatician in the Ensembl Metazoa & Plants team.
Continue readingLarge plant protein clusters accessible via gene families view
In Ensembl release 116 (Ensembl Genomes 63), two large protein clusters in Plants have incomplete or missing homology data due to production constraints. To address this, we set about making these clusters accessible via the gene families view. Please read on if you’d like to know more about these clusters, both associated with the Panther subfamily ‘PTHR11439_SF127’.
Continue readingCool stuff Ensembl VEP can do: annotate structural variants with gnomAD allele frequencies and ClinVar clinical significance
To support the filtering and interpretation of structural variants (SVs), the Ensembl VEP web interface has been extended in release 115 to annotate them with allele frequencies from gnomAD and clinical significance from ClinVar.
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