We’re looking for a software engineer to join our comparative genomics team, working on pipelines for homology and whole genome alignments. We’re looking for MScs or PhDs in computer science with experience in C/C++, containerisation and comparative genomics. Closes 7th January.
The interpretation of non-coding variants is more challenging than that of coding variants as less prediction methods and reference data are available. On top of the annotation provided for human and mouse in the Ensembl Regulatory Build, the Ensembl Variant Effect Predictor (VEP) also integrates two other human-specific datasets providing information about how variants can affect gene expression. The plugins, satMutMPRA and FunMotifs, are available for use with command-line VEP. One provides detailed information on the impact on expression of variants in the regulatory regions of disease-associated genes; the other an alternative set of genome-wide transcription factor binding motifs.
As Ensembl continues to rapidly grow in terms of the number of supported species, we continually assess our provided resources effectively match the scientific needs of the researchers using them.
In order to maintain our BioMart service at its current performance level, we will be making changes to data availability in BioMart starting with the upcoming e99 release.
Following our consultation on simplifying our GRCh37 services, we have decided to remove all support for non-human data from our dedicated GRCh37 database from release 100 onwards in early 2020. This will impact the website at grch37.ensembl.org, the REST server at rest.grch37.ensembl.org and the database at ensembldb.ensembl.org:3337. Non-human data will still be supported on the e75.ensembl.org archive.
In response to feedback during consultation, access to the full data currently provided by the existing GRCh37 REST services will also be made available for at least a year.
Please see our longer post for more details.
By default VEP will tell you the consequences for every transcript affected by a variant. You may wish to prioritise your analysis to only the most important or well supported transcripts for each gene, and VEP provides information to help you do that.
Ensembl 99 (and Ensembl Genomes 46) are due out in December and we plan to include a bumper set of new and updated species. As with all releases, we cannot guarantee that anything listed here will make it into the final release.
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.