Swiss-Prot Protein Database Daniel Amoruso December 2, 2004 BI 420

What is Swiss-Prot? Annotated sequence database established in 1986 Consists of sequence entries of different line formats Similar format to European Bioinformatics Institute Nucleotide Sequence Database (EMBL)

TrEMBL A computer annotated supplement to Swiss-Prot contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot

Distinguishing Features of Swiss- Prot Annotation Minimal Redundancy Integration with other databases Documentation

Annotation CORE DATA The sequence data The citation information (bibliographical references) The taxonomic data (description of the biological source of the protein)

Annotation- Additional Data Descriptions include: Function(s) of the protein Posttranslational modification(s) such as carbohydrates, phosphorylation, acetylation and GPI-anchor Domains and sites, for example, calcium-binding regions, ATP-binding sites, zinc fingers, homeoboxes, and SH2 and SH3 domains Secondary structure, e.g. alpha helix, beta sheet Quaternary structure, i.g. homodimer, heterotrimer, etc. Similarities to other proteins Disease(s) associated with any number of deficiencies in the protein Sequence conflicts, variants, etc.

Minimal Redundancy Much of data comes from more than one literature report Data condensed and merged to appear more concise and coherent Conflicts in data are listed for each entry

Integration with other databases 50+ databases for cross-reference Nucleic acid sequences, protein tertiary structure, protein 3-D models, etc. Allows Swiss-PROT to play a major role as the focal point for biomolecular interconnectivity

Documentation All files documented and indexed Documentation kept up-to-date

Applications for the Knowledgebase Provides highly organized data and information on a wide variety of proteins Can be used as a starting point for protein research Allows searches to be conducted starting with various search strings Biochemical encyclopedia