Some missense variants have significant impact on the protein function, some do not. In the absence of global comprehensive functional assays of missense variants, the next best way to assess if a missense variant is likely to be pathogenic is through prediction tools which take into account factors like the chemical properties of amino acids, functional protein domains and protein conservation to predict how likely it is that a missense variant will impact function. A number of different missense pathogenicity predictors are available for human through Ensembl VEP, and these are are optimised for different purposes.
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.
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.
Google Summer of Code (GSoC) is a programme that has been set up by Google to introduce students to open source software development. It links students to open source organisations such as Ensembl. The students work remotely with their GSoC project mentors during the university summer break and get paid for it by Google. Both students and organisations go through a rigorous application and selection process. It ensures that the students are among the very best and that the organisations are committed to mentoring them and their projects effectively. We think that GSoC is a great programme for students as well as Ensembl as an open source organisation and are glad that we had the opportunity to be part of it again this year!
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.
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.
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.
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.
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.