We’re pleased to announce the release of Ensembl 98, and the corresponding Ensembl Genomes release 45. We have a new Post-GWAS Analysis tool and a drove of pig and fish genomes.
Author: Emily (Outreach)
Simplifying our GRCh37 Services
We are considering the removal of support for all non-human species from the grch37.ensembl.org website and database from release 100 onwards, planned for spring next year. This is a copy of the data on our Ensembl v75 archive and has not been updated since 2014. We suggest that anyone working with non-humans switch to either the latest website at www.ensembl.org, or if you specifically need the older data currently on grch37.ensembl.org to use the e75.ensembl.org archive, which has a complete copy of all data originally released in Ensembl v75 and will remain active for the foreseeable future. If you feel that this change will have a significant impact on your analyses, please let us know.
Coming soon to an Ensembl near you: dbSNP 2.0
NCBI has announced big changes to how dbSNP manages human variation data, which will be reflected in Ensembl. These changes include a new allele normalisation approach and the removal of some older population genetics data.
Cool stuff the Ensembl VEP can do: VEP an animal
With all the fuss we make about our resources for human genomes, you might think the VEP was just for human; it’s not. We have really useful resources, like SIFT, phenotypes and caches for loads of other species in Ensembl.
What’s coming up in Ensembl release 98?
Ensembl 98 (and Ensembl Genomes 45) are due out next month, so it’s time to pig-out on the tasty morsels we have to offer. As with all releases, we cannot guarantee that anything listed here will make it into the final release.
Retirement of Ensembl archive 76
The archive website for Ensembl 76 will be retired with the release of Ensembl 98 in the Autumn. This is inline with our rolling retirement policy, where archives are retired after five years, unless they contain the last instance of an important dataset for a key species.
The database will still be available for direct queries and on our FTP site.
Cool stuff the Ensembl VEP can do: parse protein HGVS
HGVS notation is an excellent way to describe variants in proteins, and VEP can interpret variants described this way to see if they are already known or if they affect other genomic features, so long as there is enough information to find a unique genomic location. If there isn’t, the Variant Recoder can help you to find the variant you need.
Cool stuff the Ensembl VEP can do: where in a transcript?
Interpreting a single variant can be a lot more involved than just finding out its consequence. Sometimes to understand a variant, you need to know exactly where it falls, which exon, which amino acid, sometimes even which base in the codon. The VEP gives you all of this by default.
Your input into Ensembl’s new design
Work continues on our exciting new website, which is available as a pre-alpha release. We’ve been consulting with some of you in various ways, such as interviews and meetings, because we want to make sure that the new Ensembl serves your needs. We’re now asking for your help with a short survey, which will just take a couple of minutes to fill in. Plus, you can enter into a draw to win an EMBL-EBI t-shirt.
Cool stuff the Ensembl VEP can do: check conservation
If you’re really delving into the role of a particular genetic variant, you might want to know about that base position in other species. VEP can get you ancestral alleles in human and conservation scores in many species for a variant position allowing you to assess if a position is evolutionarily important, or if an allele matches our primate ancestors.