Often, people want to search InterPro with a batch of amino acid sequences - for example, to analyse whole genomes or proteomes. There are two ways in which it is possible to do this. The first way involves downloading and installing the InterProScan analysis tool. This can be obtained from here.
The software comes with full installation instructions. It also has a lot of configurable features, including the ability to search nucleic acid sequences against the database.
The second way of searching InterPro with a batch of sequences involves the use of the EBI's web services. These allow up to 25 sequences to be analysed per request. Instructions on how to use the SOAP-based web service are available here.