Genetic variation between individuals results in a range of human phenotypes. Variants that fall within coding regions of genes generally have direct effects on the proteins encoded by the genes with which they overlap. This six-hour virtual workshop will provide participants with an opportunity to gain hands-on experience of using EMBL-EBI tools and resources to assess the effects of genetic variants on the structure and function of proteins in a common workflow. 

During the course, a single example will be used throughout, using different EMBL-EBI tools and resources at each stage of the analysis pipeline. The example will involve running a VCF file through the Ensembl Variant Effect Predictor (VEP), then following links to UniProt, PDBe, and AlphaFoldDB for further variant information and interpretation. 

Virtual course

This course will take place on Zoom. Trainers will be available to assist during practical sessions, answer questions, and provide further explanations during the Zoom.

To join the course you will need to create an EMBL-EBI Training website account.

Who is this course for?

This course is aimed at wet-lab scientists and bioinformaticians who would like to use EMBL-EBI data resources to interpret the effects of genetic variants on protein structure and function.

What will I learn?

Learning outcomes

After the course you should be able to:

• Describe the main functionality and options available for the Ensembl Variant Effect Predictor (VEP)
• Annotate a variation dataset using the web-based VEP tool
• Interpret the output of the VEP and navigate to other EMBL-EBI resources to further assess variant effects on proteins
• Access variant information in UniProt
• Identify and evaluate experimental and predicted structures representing protein variants using PDBe-KB and AlphaFoldDB (AFDB)
• Interpret the functional implications of variant-induced changes in protein structure

Course content

During this course you will learn about: 

• Ensembl and the VEP tool
• Analysis of a VCF file
• Variant information in UniProt and how it is linked to from the VEP
• The link between UniProt and PDBe-KB to identify experimental structures for those variants and compare structural conformations through the superposition tool
• The link between UniProt/PDBe-KB and AlphaFoldDB, where data/resources are showcased for variant/protein interpretation

Trainers

Please read our page on application support before starting your application. In order to gain a place on this course, you must complete the online application form.

Places will be allocated on a first-come first-served basis, so please register soon to avoid disappointment. Incomplete registrations will not be processed.