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

  1. William R. Pearson

Published Online: 1 JUN 2013

DOI: 10.1002/0471250953.bi0301s42

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Pearson, W. R. 2013. An Introduction to Sequence Similarity (“Homology”) Searching. Current Protocols in Bioinformatics. 42:3.1:3.1.1–3.1.8.

Author Information

  1. University of Virginia School of Medicine, Charlottesville, Virginia

Publication History

  1. Published Online: 1 JUN 2013


Sequence similarity searching, typically with BLAST, is the most widely used and most reliable strategy for characterizing newly determined sequences. Sequence similarity searches can identify “homologous” proteins or genes by detecting excess similarity— statistically significant similarity that reflects common ancestry. This unit provides an overview of the inference of homology from significant similarity, and introduces other units in this chapter that provide more details on effective strategies for identifying homologs. Curr. Protoc. Bioinform. 42:3.1.1-3.1.8. © 2013 by John Wiley & Sons, Inc.


  • sequence similarity;
  • homology;
  • orthlogy;
  • paralogy;
  • sequence alignment;
  • multiple alignment;
  • sequence evolution