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

2. 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) • http://us.expasy.org/sprot/sprot-top.html

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

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

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

6. 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.

7. 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

8. 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

9. Documentation • All files documented and indexed • Documentation kept up-to-date

10. 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