UNIT 3.1 An Introduction to Sequence Similarity (“Homology”) Searching

  1. Gary D. Stormo

Published Online: 1 SEP 2009

DOI: 10.1002/0471250953.bi0301s27

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Stormo, G. D. 2009. An Introduction to Sequence Similarity (“Homology”) Searching. Current Protocols in Bioinformatics. 27:3.1:3.1.1–3.1.7.

Author Information

  1. Washington University, School of Medicine, St. Louis, Missouri

Publication History

  1. Published Online: 1 SEP 2009
  2. Published Print: SEP 2009

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Homologous sequences usually have the same, or very similar, functions, so new sequences can be reliably assigned functions if homologous sequences with known functions can be identified. Homology is inferred based on sequence similarity, and many methods have been developed to identify sequences that have statistically significant similarity. This unit provides an overview of some of the basic issues in identifying similarity among sequences and points out other units in this chapter that describe specific programs that are useful for this task. Curr. Protoc. Bioinform. 27:3.1.1-3.1.7. © 2009 by John Wiley & Sons, Inc.


  • sequence similarity;
  • homology;
  • dynamic programming;
  • similarity-scoring matrices;
  • sequence alignment;
  • multiple alignment;
  • sequence evolution