Cool stuff Ensembl VEP can do: protein annotations from neXtProt

Together with the neXtProt team, we’ve created a plugin for the command-line VEP tool to retrieve and report information about the protein location of missense and stop gained variants.

Science relies on cooperation and teamwork, and the data and tools available in Ensembl certainly rely on collaborations with many other groups and consortia.

Ensembl is part of the European Joint Programme on Rare Diseases (EJP RD) –  a community which aims to improve patient outcomes by creating a comprehensive, sustainable ecosystem linking research, care and medical innovation.

Within the EJP RD, we’ve teamed up with the neXtProt group, who provide an integrative resource for information on human proteins. They pull in data from key resources including UniProt, IntAct and the Human Protein Atlas and combine this with information curated from the literature. Annotations available for protein positions include structural and functional information such as if a loci lies in a helical region or if an amino acid is directly involved in the activity of an enzyme.

These data are valuable for variant interpretation. Together with the neXtProt team, we’ve created a plugin for the command-line VEP tool to retrieve and report information about the protein location of missense and stop gained variants. The plugin can be configured to return only specific types of information, for example ‘BindingSite’ and ‘CleavageSite’. The plugin queries the neXtProt SPARQL endpoint on the fly which means the latest data is always available, but it takes a little time, making it more suitable for smaller sets of a few hundred variants, rather than whole exomes.

Leave a Reply

Your email address will not be published. Required fields are marked *