Standard Article

Pattern Searches in Protein Sequences

  1. Dominique Koua,
  2. Frédérique Lisacek

Published Online: 15 JUN 2012

DOI: 10.1002/9780470015902.a0006222.pub2

eLS

eLS

How to Cite

Koua, D. and Lisacek, F. 2012. Pattern Searches in Protein Sequences. eLS. .

Author Information

  1. SIB Swiss Institute of Bioinformatics, Geneva, Switzerland

Publication History

  1. Published Online: 15 JUN 2012

Abstract

Common amino acid patterns characterise protein families. The results of automated searches for such patterns are used to qualify protein structure and function and to explore evolutionary relationships. Considering the increasing number of deoxyribonucleic acid (DNA) and protein sequences generated by high-throughput technologies, pattern search is commonly undertaken in the identification of new protein function or the elucidation of biological processes. A wide array of pattern matching methods has been implemented. They aim at identifying the constraints governing the occurrence of amino acids in protein regions. These constraints are expressed as probabilities or as templates or both to set the basis of automated search.

Key Concepts:

  • Protein families are structured on the basis of common sequence patterns.

  • Patterns constrain the nature and the position of amino acids.

  • Patterns are matched to templates called signatures or profiles.

  • Computing significant scores in addition to building realistic predictive models are the basic requirements for accurate identification by pattern matching.

Keywords:

  • motif;
  • pattern;
  • fingerprint;
  • signature;
  • profile;
  • domain;
  • protein family;
  • pattern matching