Frequently asked questions (FAQs)

How can I ensure privacy for my sequence searches?

We adhere to EMBL standards on data privacy. However, if you have privacy concerns about submitting sequences for analysis via the web, the InterProScan software package can be downloaded for local installation from the EBI's FTP server.

Can I access InterProScan programmatically?

InterProScan can be accessed programmatically via Web services that allow up to one sequence per request, and up to 25 requests in parallel (both SOAP and REST-based services are available).

How do I interpret my InterProScan results?

Please see the online tutorials section on the Training & tutorials page.

What are entry types and why are they important?

Each InterPro entry is assigned one of a number of types which tell you what you can infer when a protein matches the entry. The entry types are:

  • Homologous superfamily

    Homologous Superfamily

    A homologous superfamily is a group of proteins that share a common evolutionary origin, reflected by similarity in their structure. Since superfamily members often display very low similarity at the sequence level, this type of InterPro entry is usually based on a collection of underlying hidden Markov models, rather than a single signature.
  • Family


    A protein family is a group of proteins that share a common evolutionary origin reflected by their related functions, similarities in sequence, or similar primary, secondary or tertiary structure. A match to an InterPro entry of this type indicates membership of a protein family.
  • Domain


    Domains are distinct functional, structural or sequence units that may exist in a variety of biological contexts. A match to an InterPro entry of this type indicates the presence of a domain.
  • Repeat


    A match to an InterPro entry of this type identifies a short sequence that is typically repeated within a protein.
  • Site


    A match to an InterPro entry of this type indicates a short sequence that contains one or more conserved residues. The type of sites covered by InterPro are active sites, binding sites, post-translational modification sites and conserved sites.

In addition to signatures that have been grouped into InterPro entries, you can also find unintegrated signatures that might not yet be curated or might not reach InterPro's standards for integration. However, they may provide information about a protein.

What are entry relationships?

InterPro organises its content into hierarchies, where possible. Entries at the top of these hierarchies describe broad families or domains that share higher level structure and/or function, while those entries at the bottom describe more specific functional subfamilies or structural/functional subclasses of domains.

Entry relationships example

For example, steroid hormone receptors constitute a family of nuclear receptors responsible for signal transduction mediated by steroid hormones, and can be sub-classified into different groups, including the liver X receptor subfamily. This subfamily consists of nuclear receptors that regulate the metabolism of several important lipids, including oxysterols.

What are overlapping entries?

On the entry page, the relationship between homologous superfamilies and other InterPro entries is calculated by analysing the overlap between matched sequence sets. An InterPro entry is considered related to a homologous superfamily if its sequence matches overlap (i.e., the match positions fall within the homologous superfamily boundaries) and either the Jaccard index (equivalent) or containment index (parent/child) of the matching sequence sets is greater than 0.75.

What do the colours mean in the graphical view of matches to my protein?

The graphical view of InterPro matches show where the signatures that match your protein appear on the sequence. There are two ways that these graphical "blobs" can be coloured.

If you select "Colour by: domain relationship", in the left hand menu, the domains that are from the same or related InterPro entries will be coloured the same, allowing easy visualisation of domains we know to be related. Unintegrated signatures will always be grey blobs, family signatures will always be shown as white, and sites will always be black when this option is selected.

If you select "Colour by: member database", each blob in the sequence features section will be coloured according to the member database that provides the signature, as shown in this diagram. However, the sequence summary view will retain the domain relationship colour scheme.

Why are there no e-values associated with InterPro entries?

The signatures contained within InterPro are produced in different ways by different member databases, so their e-values and/or scoring systems cannot be meaningfully compared or combined. For this reason, we do not show e-values on the InterPro web site. However, e-values can be obtained via the downloadable InterProScan software package, which outputs detailed individual results for each member database sequence analysis algorithm.

Can I trust my sequence search results?

We make every effort to ensure that signatures integrated into InterPro are accurate. Before being integrated, signatures are manually checked by curators to ensure that they are of a high quality (i.e., they match the proteins they are supposed to and hit as few incorrect proteins as possible).

While matches to InterPro should therefore be trustworthy, there are some caveats. Most proteins are currently uncharacterised, so quality checks can only ever be based on the subset of characterised proteins that match the signature. It is therefore possible that signatures can match false positives that have not been detected.

A useful rule of thumb is that the more signatures within an InterPro entry that match a protein, the more likely it is that the match is correct. Matches within the same hierarchy would also tend to increase confidence, as they all imply membership of a particular group.

Nevertheless, please bear in mind that the member database signatures are computational predictions. If you think one of our signatures matches false positives, please contact us.

How are InterPro entries mapped to GO terms?

The assignment of GO terms to InterPro entries is performed manually, and is an ongoing process (view related publication).

How do I download InterPro?

The database and related software are freely available from the ftp site for download and distribution, provided the following Copyright line notice is supplied: InterPro - Integrated Resource Of Protein Domains And Functional Sites. Copyright (C) 2001 The InterPro Consortium.

How do I contribute?

We welcome your contributions. We encourage you to use the Add your annotation button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries. To report errors or problems with the database, please get in touch via EBI support.

How do I collaborate?

If you are interested in potential collaborations with InterPro, please contact us via EBI support.