Using OrthoCluster for the Detection of Synteny Blocks Among Multiple Genomes

Ismael A. Vergara1, Nansheng Chen1

1 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 6.10
DOI:  10.1002/0471250953.bi0610s27
Online Posting Date:  September, 2009
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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.

Keywords: OrthoCluster; OrthoClusterDB; InParanoid; MultiParanoid; genome painter; GBrowse; segmental duplication

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Table of Contents

  • Introduction
  • Files
  • Basic Protocol 1: Using OrthoCluster via Web Interface with User‐Defined Datasets and Parameters
  • Basic Protocol 2: Using OrthoCluster via Web Interface with Predefined Datasets and Parameters
  • Basic Protocol 3: Using OrthoCluster Locally for the Detection of Synteny Blocks
  • Alternate Protocol 1: Using OrthoCluster for the Detection of Segmental Duplications
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

Literature Cited
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