UNIT 3.1 An Overview of Sequence Similarity (“Homology”) Searching

  1. Daniel B. Davison

Published Online: 1 AUG 2002

DOI: 10.1002/0471250953.bi0301s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Davison, D. B. 2002. An Overview of Sequence Similarity (“Homology”) Searching. Current Protocols in Bioinformatics. 00:3.1:3.1.1–3.1.7.

Author Information

  1. Bristol-Myers Squibb Pharmaceutical Research Institute, Hopewell, New Jersey

Publication History

  1. Published Online: 1 AUG 2002
  2. Published Print: JAN 2003

This is not the most recent version of the article. View current version (1 JUN 2013)


Sequence similarity searching is an essential tool for molecular biologists. It is used to support inference of protein function and for phylogenetic analysis. Every searching procedure requires some understanding of the underlying principles, so at the very least the investigator's selection of parameters is correct. The principles underlying the most commonly used procedures are presented in this unit. The discussion is intentionally non-mathematical, but does contain references for those who desire a mathematical and statistical discussion of these procedures.