UNIT 6.10 Using OrthoCluster for the Detection of Synteny Blocks Among Multiple Genomes

  1. Ismael A. Vergara,
  2. Nansheng Chen

Published Online: 1 SEP 2009

DOI: 10.1002/0471250953.bi0610s27

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Vergara, I. A. and Chen, N. 2009. Using OrthoCluster for the Detection of Synteny Blocks Among Multiple Genomes. Current Protocols in Bioinformatics. 27:6.10:6.10.1–6.10.18.

Author Information

  1. Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada

Publication History

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


Synteny blocks are composed of two or more orthologous genes conserved among species, resulting from speciation from their last common ancestor. OrthoCluster (Zeng et al., 2008) is a fast and easy-to-use program for the identification of synteny blocks among multiple genomes. It allows users to identify synteny blocks that contain different types of mismatches, and to decide whether they require conservation of gene orientation and conservation of gene order within the blocks. OrthoCluster can also be used to find duplicated blocks within genomes. Although genes and their correspondence are usually used as input for OrthoCluster, in fact, OrthoCluster can be applied using any type of markers as input as long as their relationships can be established. OrthoClusterDB provides a Web interface for running OrthoCluster with user-defined datasets and parameters, as well as for browsing and downloading precomputed synteny blocks for different groups of genomes. Curr. Protoc. Bioinform. 27:6.10.1-6.10.18. © 2009 by John Wiley & Sons, Inc.


  • OrthoCluster;
  • OrthoClusterDB;
  • InParanoid;
  • MultiParanoid;
  • genome painter;
  • GBrowse;
  • segmental duplication