A new view on proteins

Data visualisation and integration have become increasingly important as biological data continues to grow at exponential rates. Indeed, they have become essential tools for bringing to light information that might be otherwise hidden, unclear or difficult to grasp. A new visual approach by UniProt, the universal protein resource, presents protein sequence features in one compact view using a highly interactive BioJS component. This is the first visualisation feature in a public resource that lets users see different types of protein sequence features such as domains, sites, PTMs and natural variants from multiple sources in a single view.

'We are experiencing an unprecedented increase in genomic and protein data, and its interpretation depends more than ever on innovative and integrative tools to aid with scientific discovery," says EMBL-EBI UniProt Development team leader Maria Martin. "Genomic browsers enable researchers to explore genomic information, but these tools haven't been available for proteins, the essential functional units of living organisms. There has been a real need for this feature, as it is impossible to interpret genomes without knowing about the proteins they encode. The UniProt sequence viewer is a tremendous step forward in the interpretation of the biology of living organisms."

The variants track, part of the feature viewer, provides a new way of displaying a large number of variants within a small space. It gives users a quick overview of areas where there is a lot of variation, insertions and deletions. Data in the variants track includes UniProt curated natural variants along with imported variants from large-scale studies such as the 1000 Genomes Project, ExAC, ESP and COSMIC.

Similar to genome viewers, the UniProt feature viewer displays information on tracks. Each track presents a biological category of features, and can be expanded into sub-tracks for a more compact overview.

Keep it in site

Showing all co-localised sequence features in one view makes it easier to spot patterns and make inferences. Figure 2 shows an example of how you might use the feature viewer. To investigate the human Lipoprotein lipase enzyme’s involvement in the Lipoprotein lipase deficiency (LPL deficiency), you can click on the "Domain & sites" label and see that there are three active sites. If you want to investigate the potential effect of variants on these sites, click on the "Variants" label to open up the track. You can zoom into the active sites and click on them to see all their positions highlighted across all protein features. This unique functionality lets you view possible variant implications at a glance.

A view on variants

Figure 3 shows how you might see whether a variant plays a role in disease. Clicking on the second active site at position 183 highlights three disease variants in the same position. This shows that the variants are impacting the active site, indicating that they play a role in the disease. Clicking on the variant dots opens up an information box with links to relevant publications.

The UniProt feature viewer is available for every UniProt KnowledgeBase (UniProtKB) protein entry. Under the "Display" heading, follow the "Feature viewer" link.

Want to integrate the feature viewer into your website?

The UniProt feature viewer can be integrated into any website. You can choose to keep all available tracks or only those most relevant to you.

If you would like to include the feature viewer in your own website or resource, you can find instructions in our technical documentation.