In addition to the web-based sequence, text and BioMart searches, you can download both the InterPro data and the InterProScan analysis tool via anonymous FTP  and run InterProScan locally. We would recommend this if you have a large number of searches to perform, or are concerned about confidentiality. Additional files that are available on the FTP site include a list of all InterPro entries of each type, a file of InterPro mappings to GO terms, and a list of InterPro hits in UniProtKB. The database and matches are available in XML format with a corresponding document type definition (DTD) file.
Searching InterPro 
You can search InterPro using:
- sequence search, which uses the InterProScan  analysis tool to predict the family and domain information for an amino acid sequence;
- text search, using InterPro entry names and identifiers, UniProt  accessions, GO  terms, PDB  identifiers, or free text, to find information in InterPro relating to your query;
- BioMart, which provides more flexible and powerful querying of InterPro data and links to other protein resources such as PRIDE and Reactome. The BioMart includes signature matches to both UniProtKB  and UniParc  proteins, and results can be retrieved in HTML, plain text or in Microsoft Excel spreadsheet format.
Figure 2 highlights the location of the different search entry points on the InterPro web interface.
InterPro matches to proteins are displayed graphically (illustrated in Figure 3). The coloured bars indicate the location of signature matches on the protein sequences. Each matching InterPro entry is displayed on a separate line. Bars of the same colour indicate relationships between the entries.
The protein family membership section (see figure) provides information about the family to which the protein is predicted to belong. The domain and repeats section summarises the predicted composition of the protein. All signatures -and the InterPro entries where they are integrated- are displayed in the detailed signature matches. Visualilisation of the signatures matches can be filtered by type (family, domain, repeat, site); status (integrated in InterPro or unintegrated); or color (based on domain relationship or member database).
You can access further information in an InterPro entry by clicking on the links, which will take you to the corresponding database entries.