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Department of Zoology, GACW (2018-2019)
SWISS-PROT- Protein Database
INTRODUCTION
The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the
collection of functional information on proteins.
It consists of two sections:
UniProtKB/Swiss-Prot
Introduction:
UniProtKB/Swiss-Prot is the manually annotated and reviewed section of the UniProt
Knowledgebase (UniProtKB). The SWISS-PROT Protein Knowledgebase is an annotated
protein sequence database established in 1986. It is maintained collaboratively by the Swiss
Institute for Bioinformatics (SIB) and the European Bioinformatics Institute (EBI).
Features ofSwiss-Prot
The SWISS-PROT Protein Knowledgebase is a curated protein sequence database that provides
a high level of
UniProt
Swiss -Prot
• Reviewed
• Manually annotated
• Records with information
extracted from literature and
curator-evaluated computational
analysis.
Tr-EMBL (Transalted European
Molecular Biological Labratory)
• Unreviewed
• Computationally annotated
• Records that await full manual
annotation.
Department of Zoology, GACW (2018-2019)
(i) Annotations
(ii) Minimal redundancy and
(iii) Integration with other databases.
Annotation:
In SWISS-PROT two classes of data can be distinguished:
 Core data
 Annotation data
Core data:
The core data consists of the following information:
 The citation information (bibliographical references)
 The taxonomic data (description of the biological source of the protein),
Annotation Data:
The annotation consists of the description of the following items:
 Function(s) of the protein
 Post-translational modification(s). For example carbohydrates, phosphorylation,
acetylation, GPI-anchor, etc.
 Domains and sites. For example calcium binding regions, ATP-binding sites, zinc
fingers, homeoboxes, SH2 and SH3 domains, etc.
 Secondary structure. For example alpha helix, beta sheet, etc.
 Quaternary structure. For example homodimer, heterotrimer, etc.
 Similarities to other proteins
 Disease(s) associated with deficiencie(s) in the protein
Department of Zoology, GACW (2018-2019)
 Sequence conflicts, variants, etc.
Minimal redundancy
Many sequence databases contain, for a given protein sequence, separate entries which
correspond to different literature reports.
In SWISS-PROT they try to merge all these data so as to minimise the redundancy of the
database.
 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
 Swiss-Prot provides cross-references to external data collections
 Integration between the three types of sequence-related databases (nucleic acid
sequences, protein sequences and protein tertiary structures)
 It’s integrated with EMBL, PDB, OMIM, Pfam and PROSITE etc.
Documentation
 All files documented and indexed.
 Documentation kept up-to-date.
Conclusion
 Swiss-Prot continuously enhanced its format and content to adjust to the wide knowledge
pool in proteomics along with high quality of annotation.
 Automated annotation procedures are used for Swiss-Prot in a very conservative manner.
 The extensive integration of SWISS-PROT with specialized databases enables users to
navigate through the current knowledge in the Life Sciences providing an insight into the
universe of proteins.

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Swiss PROT

  • 1. Department of Zoology, GACW (2018-2019) SWISS-PROT- Protein Database INTRODUCTION The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins. It consists of two sections: UniProtKB/Swiss-Prot Introduction: UniProtKB/Swiss-Prot is the manually annotated and reviewed section of the UniProt Knowledgebase (UniProtKB). The SWISS-PROT Protein Knowledgebase is an annotated protein sequence database established in 1986. It is maintained collaboratively by the Swiss Institute for Bioinformatics (SIB) and the European Bioinformatics Institute (EBI). Features ofSwiss-Prot The SWISS-PROT Protein Knowledgebase is a curated protein sequence database that provides a high level of UniProt Swiss -Prot • Reviewed • Manually annotated • Records with information extracted from literature and curator-evaluated computational analysis. Tr-EMBL (Transalted European Molecular Biological Labratory) • Unreviewed • Computationally annotated • Records that await full manual annotation.
  • 2. Department of Zoology, GACW (2018-2019) (i) Annotations (ii) Minimal redundancy and (iii) Integration with other databases. Annotation: In SWISS-PROT two classes of data can be distinguished:  Core data  Annotation data Core data: The core data consists of the following information:  The citation information (bibliographical references)  The taxonomic data (description of the biological source of the protein), Annotation Data: The annotation consists of the description of the following items:  Function(s) of the protein  Post-translational modification(s). For example carbohydrates, phosphorylation, acetylation, GPI-anchor, etc.  Domains and sites. For example calcium binding regions, ATP-binding sites, zinc fingers, homeoboxes, SH2 and SH3 domains, etc.  Secondary structure. For example alpha helix, beta sheet, etc.  Quaternary structure. For example homodimer, heterotrimer, etc.  Similarities to other proteins  Disease(s) associated with deficiencie(s) in the protein
  • 3. Department of Zoology, GACW (2018-2019)  Sequence conflicts, variants, etc. Minimal redundancy Many sequence databases contain, for a given protein sequence, separate entries which correspond to different literature reports. In SWISS-PROT they try to merge all these data so as to minimise the redundancy of the database.  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  Swiss-Prot provides cross-references to external data collections  Integration between the three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures)  It’s integrated with EMBL, PDB, OMIM, Pfam and PROSITE etc. Documentation  All files documented and indexed.  Documentation kept up-to-date. Conclusion  Swiss-Prot continuously enhanced its format and content to adjust to the wide knowledge pool in proteomics along with high quality of annotation.  Automated annotation procedures are used for Swiss-Prot in a very conservative manner.  The extensive integration of SWISS-PROT with specialized databases enables users to navigate through the current knowledge in the Life Sciences providing an insight into the universe of proteins.