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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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