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The PIR SuperFamily (PIRSF) classification system

Part 3. Proteomics

3.6. Proteome Families

Short Specialist Review

  1. Winona C. Barker1,
  2. Raja Mazumder2,
  3. Anastasia N. Nikolskaya2,
  4. Cathy H. Wu2

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g306302

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Barker, W. C., Mazumder, R., Nikolskaya, A. N. and Wu, C. H. 2005. The PIR SuperFamily (PIRSF) classification system. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.6:87.

Author Information

  1. 1

    National Biomedical Research Foundation, Washington, DC, USA

  2. 2

    Georgetown University Medical Center, Washington, DC, USA

Publication History

  1. Published Online: 15 APR 2005


Protein family classification provides effective means for large-scale genome annotation and biological knowledge discovery based on the information embedded within families of homologous sequences and their structures. The Protein Information Resource (PIR) developed the PIRSF (SuperFamily) system, a network classification system based on evolutionary relationship of full-length proteins, to facilitate the propagation and standardization of protein annotation. Sequence analysis and protein classification based on full-length proteins, including the preservation of domain architecture, can lead to educated predictions for both generic biochemical and specific biological functions. The multiple levels of sequence diversity, from superfamilies to subfamilies, reflect different degrees of functional granularity and, thereby, allow more accurate propagation of annotation and the development of standard protein nomenclature and ontology. The PIRSF database is integrated with other family, function, and structural classification schemes, and is accessible at for report retrieval and sequence classification.


  • protein annotation;
  • protein domains;
  • protein evolution;
  • protein family classification;
  • protein function;
  • Protein Information Resource (PIR);
  • protein superfamilies;
  • UniProt