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Classification of proteins into families

Part 3. Proteomics

3.6. Proteome Families

Introductory Review

  1. Nicola J. Mulder,
  2. Rolf Apweiler

Published Online: 15 JAN 2005

DOI: 10.1002/047001153X.g306109

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Mulder, N. J. and Apweiler, R. 2005. Classification of proteins into families. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.6:78.

Author Information

  1. European Bioinformatics Institute, Cambridge, UK

Publication History

  1. Published Online: 15 JAN 2005

Abstract

Functional annotation of proteins is vital for a thorough understanding of genomic systems, diseases, and pathogenesis. With the genome era in full swing, thousands of new sequences from genome sequencing projects are available, but they cannot be manually annotated. Reliable methods for automatic functional classification of proteins are being developed. The most useful tools use various methods for identifying motifs or domains found in previously characterized protein families. Protein families can be classified using two main approaches: sequence clustering and protein signatures. Once members of a protein family are discovered, inference of functional annotation to all members is possible. This chapter reviews the existing methods using these approaches and the major databases in the public domain that implement the methods.

Keywords:

  • protein family;
  • signature;
  • clustering;
  • functional classification;
  • hidden Markov model;
  • regular expression;
  • profile