InterProScan is a tool that integrates various protein signature recognition methods from the InterPro consortium databases into a single resource. It supports both protein and DNA sequence analysis and is accessible via a web interface, standalone Perl version, and a SOAP Web Service. The tool helps in characterizing the physiochemical properties and potential relationships of protein sequences by searching against secondary databases that contain overlapping information on protein families, domains, and functional sites. The input form allows users to specify their desired output format, choose specific methods, and provide sequence input. The output includes graphical and tabular views, with links to detailed descriptions in the InterPro databases. The standalone version of InterProScan is available for download and can run on single or multiple machines, supporting various queuing systems. The tool is freely available to academic and commercial organizations, with documentation and support provided by the European Bioinformatics Institute (EBI).InterProScan is a tool that integrates various protein signature recognition methods from the InterPro consortium databases into a single resource. It supports both protein and DNA sequence analysis and is accessible via a web interface, standalone Perl version, and a SOAP Web Service. The tool helps in characterizing the physiochemical properties and potential relationships of protein sequences by searching against secondary databases that contain overlapping information on protein families, domains, and functional sites. The input form allows users to specify their desired output format, choose specific methods, and provide sequence input. The output includes graphical and tabular views, with links to detailed descriptions in the InterPro databases. The standalone version of InterProScan is available for download and can run on single or multiple machines, supporting various queuing systems. The tool is freely available to academic and commercial organizations, with documentation and support provided by the European Bioinformatics Institute (EBI).