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Swiss-Prot Protein
Database
Dr. Ayaz Ahmad
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)
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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
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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, e.g. homodimer, heterotrimer, etc.
• Similarities to other proteins
• Disease(s) associated with any number of deficiencies in
the protein
• Sequence conflicts, variants, etc.
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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
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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
