The MEROPS database is an integrated resource for peptidases (proteases), their inhibitors, and substrates. It uses a hierarchical classification system to group peptidases and inhibitors into protein species, families, and clans. The database focuses on distinguishing peptidases based on their cleavage specificity and inhibitor interactions. Over 39,000 cleavage sites in proteins, peptides, and synthetic substrates have been collected, enabling the display of peptidase specificity and substrate alignments. The database has been updated to include analysis tools for genome comparisons, highlighting significant gains and losses of peptidase genes across species. The database includes a hierarchical classification system, with families containing proteins related by sequence and clans containing proteins with distant relationships visible only through structure. The database also provides domain architecture displays, substrate cleavage data, and specificity information. The MEROPS database includes extensive bibliographic references and cross-references to other databases. It also includes a distributed annotation system (DAS) server for data extraction and a community annotation feature for user submissions. The database has been enhanced with features such as chromosomal location information for eukaryotes with fully sequenced genomes, improved displays of peptidase distribution, and the ability to order tables by identifier or protein name. The database also includes a new index of gene names and a substrate menu for easier access to substrates with known cleavages. The database is updated quarterly and users can subscribe to the MEROPS blog for updates. The database includes tools for dynamic alignment of substrate sequences and displays of peptidase specificity, including WebLogo and frequency matrices. The database is supported by the Wellcome Trust and includes references to numerous scientific publications.The MEROPS database is an integrated resource for peptidases (proteases), their inhibitors, and substrates. It uses a hierarchical classification system to group peptidases and inhibitors into protein species, families, and clans. The database focuses on distinguishing peptidases based on their cleavage specificity and inhibitor interactions. Over 39,000 cleavage sites in proteins, peptides, and synthetic substrates have been collected, enabling the display of peptidase specificity and substrate alignments. The database has been updated to include analysis tools for genome comparisons, highlighting significant gains and losses of peptidase genes across species. The database includes a hierarchical classification system, with families containing proteins related by sequence and clans containing proteins with distant relationships visible only through structure. The database also provides domain architecture displays, substrate cleavage data, and specificity information. The MEROPS database includes extensive bibliographic references and cross-references to other databases. It also includes a distributed annotation system (DAS) server for data extraction and a community annotation feature for user submissions. The database has been enhanced with features such as chromosomal location information for eukaryotes with fully sequenced genomes, improved displays of peptidase distribution, and the ability to order tables by identifier or protein name. The database also includes a new index of gene names and a substrate menu for easier access to substrates with known cleavages. The database is updated quarterly and users can subscribe to the MEROPS blog for updates. The database includes tools for dynamic alignment of substrate sequences and displays of peptidase specificity, including WebLogo and frequency matrices. The database is supported by the Wellcome Trust and includes references to numerous scientific publications.