Unit

UNIT 9.12 Using the Generic Synteny Browser (GBrowse_syn)

  1. Sheldon J. McKay1,2,
  2. Ismael A. Vergara3,
  3. Jason E. Stajich4

Published Online: 1 SEP 2010

DOI: 10.1002/0471250953.bi0912s31

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

McKay, S. J., Vergara, I. A. and Stajich, J. E. 2010. Using the Generic Synteny Browser (GBrowse_syn). Current Protocols in Bioinformatics. 31:9.12:9.12.1–9.12.25.

Author Information

  1. 1

    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

  2. 2

    University of Arizona, Tucson, Arizona

  3. 3

    Simon Fraser University, Burnaby, British Columbia, Canada

  4. 4

    University of California Riverside, Riverside, California

Publication History

  1. Published Online: 1 SEP 2010
  2. Published Print: SEP 2010

Abstract

Genome Browsers are software that allow the user to view genome annotations in the context of a reference sequence, such as a chromosome, contig, scaffold, etc. The Generic Genome Browser (GBrowse) is an open-source genome browser package developed as part of the Generic Model Database Project (see unit Unavailable ; Stein et al., 2002). The increasing number of sequenced genomes has led to a corresponding growth in the field of comparative genomics, which requires methods to view and compare multiple genomes. Using the same software framework as GBrowse, the Generic Synteny Browser (GBrowse_syn) allows the comparison of colinear regions of multiple genomes using the familiar GBrowse-style Web page. Like GBrowse, GBrowse_syn can be configured to display any organism, and is currently the synteny browser used for model organisms such as C. elegans (WormBase; http://www.wormbase.org; see unit Unavailable ) and Arabidopsis (TAIR; http://www.arabidopsis.org; see unit Unavailable ). GBrowse_syn is part of the GBrowse software package and can be downloaded from the Web and run on any Unix-like operating system, such as Linux, Solaris, or MacOS X. GBrowse_syn is still under active development. This unit will cover installation and configuration as part of the current stable version of GBrowse (v. 1.71). Curr. Protoc. Bioinform. 31:9.12.1-9.12.25. © 2010 by John Wiley & Sons, Inc.

Keywords:

  • G Browse;
  • Genome Browser;
  • Synteny