InterProScan is a tool that integrates multiple protein signature recognition methods from the InterPro consortium member databases into one resource. It allows the analysis of both protein and DNA sequences. A web-based version is available for academic and commercial organizations at http://www.ebi.ac.uk/InterProScan/. Additionally, a standalone Perl version and a SOAP Web Service are available. Various output formats, including text tables, XML documents, and graphs, are supported. The tool is used to identify protein domains and functional sites by searching against secondary databases. The InterPro database unites these databases, which contain overlapping information on protein families, domains, and functional sites. InterPro entries are grouped based on the protein families or domains they represent. InterProScan combines the protein function recognition methods of the member databases into one application, allowing users to search for protein sequences and obtain information about their potential functions and domains. The web-based version of InterProScan allows users to submit sequences via an interactive or email method. Users can choose to submit sequences in various formats, including EMBL, SWISS, GenBank, NBRF/PIR, CODATA, Fasta, GCG, and RAW. The results can be viewed in a graphical or table format, with the graphical view displaying a cartoon of the sequence with highlighted domains or functional sites. The table view provides detailed information about matches, including sequence coordinates, E-values, and match status. A standalone version of InterProScan is available for users who wish to run their own installation. It can be run from the command line or as a CGI through a web interface. The standalone version includes a Perl core package, a data package, and a binary package precompiled for multiple platforms. It supports the use of various queuing systems, such as LSF, OpenPBS, and SGE. InterProScan is freely available to the public and is supported by the European Union under the RTD program 'Quality of Life and Management of Living Resources'. Funding for the Open Access publication charges was provided by the European Molecular Biology Laboratory (EMBL).InterProScan is a tool that integrates multiple protein signature recognition methods from the InterPro consortium member databases into one resource. It allows the analysis of both protein and DNA sequences. A web-based version is available for academic and commercial organizations at http://www.ebi.ac.uk/InterProScan/. Additionally, a standalone Perl version and a SOAP Web Service are available. Various output formats, including text tables, XML documents, and graphs, are supported. The tool is used to identify protein domains and functional sites by searching against secondary databases. The InterPro database unites these databases, which contain overlapping information on protein families, domains, and functional sites. InterPro entries are grouped based on the protein families or domains they represent. InterProScan combines the protein function recognition methods of the member databases into one application, allowing users to search for protein sequences and obtain information about their potential functions and domains. The web-based version of InterProScan allows users to submit sequences via an interactive or email method. Users can choose to submit sequences in various formats, including EMBL, SWISS, GenBank, NBRF/PIR, CODATA, Fasta, GCG, and RAW. The results can be viewed in a graphical or table format, with the graphical view displaying a cartoon of the sequence with highlighted domains or functional sites. The table view provides detailed information about matches, including sequence coordinates, E-values, and match status. A standalone version of InterProScan is available for users who wish to run their own installation. It can be run from the command line or as a CGI through a web interface. The standalone version includes a Perl core package, a data package, and a binary package precompiled for multiple platforms. It supports the use of various queuing systems, such as LSF, OpenPBS, and SGE. InterProScan is freely available to the public and is supported by the European Union under the RTD program 'Quality of Life and Management of Living Resources'. Funding for the Open Access publication charges was provided by the European Molecular Biology Laboratory (EMBL).