Pattern Searches in Protein Sequences
Published Online: 15 JUN 2012
Copyright © 2001 John Wiley & Sons, Ltd. All rights reserved.
How to Cite
Koua, D. and Lisacek, F. 2012. Pattern Searches in Protein Sequences. eLS. .
- Published Online: 15 JUN 2012
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.
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.
- protein family;
- pattern matching