SWISS-PROT is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1988, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library. Sequence data originates from three different sources: from the PIR protein sequence database, from translation of entries from the EMBL Nucleotide Database and from literature. For standardization purposes the format of SWISS-PROT follows as closely as possible that of the EMBL database.

SWISS- PROT differs from other protein databases by three fundamental criteria: A) It contains a wealth of information which are called annotations and which consist, for a given protein, in the description of its function, its post- translational modification(s), the extent of specific domains and sites of biological interest, its secondary and quaternary structures, its similarities to other proteins, the disease(s) associated with deficiencie(s) in the protein, as well as various other topics. B) Minimal redundancy.

SWISS-PROT provides a single entry for each individual sequence. Data derived from different literature reports are merged thus providing a synthetic view of the current knowledge with respect to a given protein. C) It is integrated with other databases. Cross-references are provided to many other databases including nucleotide sequence databases, the protein 3D structure database (PDB), as well as specialized data collections