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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)

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swiss prot protein database

Swiss-Prot Protein Database

Daniel Amoruso

December 2, 2004

BI 420

what is swiss prot
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
trembl
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
Distinguishing Features of Swiss-Prot
  • Annotation
  • Minimal Redundancy
  • Integration with other databases
  • Documentation
annotation
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
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
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
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
Documentation
  • All files documented and indexed
  • Documentation kept up-to-date
applications for the knowledgebase
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
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