How to search the InterPro website?

A search can be performed on the InterPro homepage using the Search box component, by clicking on the Search tab in the navigation menu, or by clicking on the magnifying glass in the navigation banner. There are five different types of search available in InterPro:

Using Browse feature to search and filter InterPro

Browse search

The browse search page can be accessed by clicking on the Browse tab in the navigation menu. The browse search provides a powerful functionality to select subsets of data available in InterPro by selecting filters according to the results required. For example, this page can be used to browse all entries which have a contributing signature from a particular member database e.g. HAMAP, or to retrieve all proteins from a certain taxon, e.g. Escherichia coli, that contain a specific domain eg OmpA-like domain.

Below we describe how to use the browse search feature:

  1. Select a data type

The browse page opens up with 7 data types to allow browsing of InterPro entries, Member databases signatures, Proteins, Structures, Taxonomies, Proteomes or Sets.

Data types
  1. Select any additional filters

The filters options displayed for each data type will vary as appropriate.

Member database filter

Member database filter

The “Select your database” option is available when Browsing by Member DB, Protein, Structure, Taxonomy and Set. It allows results to be retrieved from all or a selection of InterPro member databases. Only the databases that contain signatures for the chosen data type are displayed as options. By default all the member databases are selected, expect when Browsing by Member DB, where Pfam is the default option selected.

Text filter

The “Search entries” box allows results to be filtered to match the text entered. For example, the text could be a keyword that might be found in entry names. It also allows specific protein names or taxa to be entered. By default the term searched is highlighted in yellow in the results list, this can be disabled by clicking on the toggle icon symbol appearing between the text box and Export button once the search has started, the setting is saved and also applied to other text searches throughout the website.

Data-type specific filters

InterPro entry filters

Entry filters

When Browse by InterPro is selected, two filter types can be applied:

Member database filters

Member database filters

When Browse by Member DB is selected and a member database has been chosen, subsequent filters can be applied:

  • Member Database Entry Type: select the types of signatures required. This is dependent on the database type selected. For example, if a database contains both domains and family signatures you can filter the results for a specific type.

  • InterPro state: select all signatures from the selected database or only those signatures that have been integrated into InterPro.

Protein filters

Just as with the Member DB data type, Protein filters change based on the selection in the member database filter component. The basic filters are displayed irrespective of the selection made and an extra filter when the “All Proteins” option is selected.

Proteins filters
Database selected

If a member database has been selected, the following filters are displayed:

  • UniProt Curation: the UniProtKB is split into two sections. The reviewed set is manually curated (SwissProt) and the unreviewed set is derived from public databases automatically integrated into UniProt (TrEMBL).

  • Taxonomy: this filter allows the displayed list of proteins to be limited to certain organisms.

  • Sequence Status: this filter allows proteins to be limited to complete proteins or fragments.

All Proteins
Matching entries filter

Additionally to the filters mentioned above, when the “All Proteins” option is selected in the member database filter component, the Matching Entries filter is displayed. This filter allows the selection of proteins which do or do not contain matches to entries in the InterPro dataset.

Structure filters

Structure filters

Structure filters do not vary depending on which option has been selected in the member database filter component.

  • Experiment Type: this filter allows selection of structures based on the type of experimental data the structure is based on.

  • Resolution: this filter allows structures to be selected based on the resolution of the structure.

Data Display Options

The data display is the main part of the results section in the browse page and shows the data selected in the data type menu. The actual details shown will also be dependent on the selected data type.

Data views

Tabular view

Tabular icon

The tabular view is the default view and is available for all InterPro data types. The table view icon formats data into a tabular view composed of rows representing individual entities. The table header describes the contents of each column. Clicking on one of the rows redirects to the corresponding InterPro page.

Tabular entry view

Tabular view example for InterPro entry data type

Grid view

Grid icon

The grid view is available for all InterPro data types. It displays a series of cards summarising details of the entities being viewed. Clicking on one of the cards redirects to the corresponding InterPro page.

Grid entry view

Grid view example for InterPro entry data type

Tree view

Tree icon

The tree view is currently only enabled for taxonomy data. The tree view icon is only shown where a tree view is possible. The taxonomy tree viewer can be navigated by clicking on nodes or using keyboard arrow keys. This component is also used in the Taxonomy entry page.

Tree view

Tree view example for Euryarchaeota phylum