In Ensembl 103, and subsequent releases, we will be limiting the number of species represented in our gene trees and the BioMart data export tool. These changes are required to most effectively support our rapid growth in the number of available species.
Continue readingWhat’s coming in release 103
We’re planning to release Ensembl 103 in February 2021. We’ve got lots of plans, although we can’t guarantee everything will make it into the release.
Continue readingOpen: Ensembl Browser and REST API virtual workshops
Registration is now open for two free virtual Ensembl workshops covering the genome browser and the REST API. The Browser workshop will be held between Tuesday 26th January – Thursday 28th January 2021 (2pm-5pm) and the REST API workshop will be held between Wednesday 3rd February – Friday 5th February 2021 (2pm-4:15pm). More information and registration instructions can be found below.
Update: registration is now closed as all of the available places on the virtual Ensembl browser and REST API workshops have been filled. If you would like to be added to the waiting list, please e-mail the Ensembl Helpdesk.
Continue readingMANE progress update
NCBI and EBI have been hard at work on our joint MANE collaboration, aiming to provide a set of representative transcripts for human protein-coding genes that are identically annotated in the NCBI RefSeq and Ensembl/GENCODE annotation sets and exactly match the GRCh38 reference assembly. We released MANE v0.5 in Dec 2018, which included one well-supported MANE Select transcript for 53% of the human protein-coding genes. The remainder has required a lot more analysis and curation than we expected, but we’re pleased to announce MANE v0.92, now covering 16,865 genes or ~88% of known protein-coding genes. We’ve been focussing on clinically relevant genes and MANE Select now includes 99% of genes with high gene-disease validity. This release also includes 43 extra transcripts labeled “MANE Plus Clinical” that have been chosen to aid in clinical reporting, for example when there are additional pathogenic or likely pathogenic variants not covered in the MANE Select transcript. For example in genes where there are mutually exclusive exons and both exons have clinically relevant variants, a MANE Plus Clinical transcript will be added alongside the MANE Select transcript so that both exons are represented in MANE.
While it’s critical to consider other alternatively-spliced transcripts for variant interpretation or functional analyses, the MANE Select and MANE Plus Clinical transcripts provide a common foundation for clinical reporting, and other analyses that benefit from using just one well-supported transcript or protein per gene.
MANE Select is now shown in the genome aggregation database gnomAD v3, is displayed and used as the preferred transcript for variant reporting in ClinVar and is displayed in DECIPHER. We have released this data as a trackhub for display in the Ensembl, NCBI and UCSC genome browsers. MANE Select v0.92 transcripts will be available in Ensembl release 103 due in the Spring 2021, and will be included in BioMart and VEP.
Partnership with the community is really important to us. We value your feedback. If you are interested in working with us, please contact us at MANE-help@ebi.ac.uk.
Ensembl 102 has been released!
We are pleased to announce the release of Ensembl 102, and the corresponding release of Ensembl Genomes 49 featuring lots of new and updated data in this release including the addition of human population frequency data from the NCBI Allele Frequency Aggregator, new plant species and a large update of the available bacterial data.
Genome assemblies and annotation for many new species are also being continuously added to the Ensembl Rapid Release genome browser.
Cool stuff Ensembl VEP can do: one click BioMart
The web VEP tool gives you a lot of useful information about your variants, but you may want more details, for example about the genes your variants overlap: maybe you want to fetch their sequences, homologues or protein domains. With a single click, you can go straight to BioMart, using your list of genes or known variants as your filter.
Continue readingGene and protein families retiring
As of release 102, we will be removing the gene and protein family analysis from Ensembl. Information on related genes within and between species is still provided by our gene trees, homologues and alignments.
Continue readingTraining in the Time of Pandemic
Were you planning on attending or hosting an Ensembl workshop in 2020, but your plans got cancelled due to the SARS-CoV-2 pandemic? All is not lost, as we’re still providing live virtual training and here’s how it works.
Continue readingCool stuff Ensembl VEP can do – What’s in the cache and how does VEP use it?
We often get questions about Ensembl VEP caches – the compressed data files we create for each new Ensembl release, which can be automatically installed with the VEP installer script – so here’s a quick introduction to these handy data bundles.
Continue readingGet training, virtually
You’re invited to join us for a free, open, virtual training course, 30th November – 2nd December. The course will be held using the Blackboard training platform.
Continue reading