Using the Generic Synteny Browser (GBrowse_syn)

Sheldon J. McKay1, Ismael A. Vergara2, Jason E. Stajich3

1 University of Arizona, Tucson, Arizona, 2 Simon Fraser University, Burnaby, British Columbia, Canada, 3 University of California Riverside, Riverside, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 9.12
DOI:  10.1002/0471250953.bi0912s31
Online Posting Date:  September, 2010
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

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; 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) and Arabidopsis (TAIR; http://www.arabidopsis.org; see UNIT). 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

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Basic Protocol 1: Configuring and Using GBrowse_syn
  • Basic Protocol 2: Browsing OrthoCluster Synteny Blocks with GBrowse_syn
  • Alternate Protocol 1: Loading MERCATOR into the GBrowse_syn Database
  • Support Protocol 1: Installing GBrowse_syn in the Unix/Linux Environment
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   Bray, N. and Pachter, L. 2004. MAVID: Constrained ancestral alignment of multiple sequences. Genome Res. 14:693‐699.
   Dewey, C.N. 2006. Whole‐Genome Alignments and Polytopes for Comparative Genomics. EECS Department, University of California, Berkeley, California.
   Dewey, C.N. 2007. Aligning multiple whole genomes with Mercator and MAVID. Methods Mol. Biol. 395:221‐236.
   Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. 2003. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. U.S.A. 100:11484‐11489
   Ng, M.P., Vergara, I.A., Frech, C., Chen, Q., Zeng, X., Pei, J., and Chen, N. 2009. OrthoClusterDB: An online platform for synteny blocks. BMC Bioinformatics 10:192.
   Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003. Human‐mouse alignments with BLASTZ. Genome Res. 13:103‐107.
   Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12:1599‐1610.
   Zeng, X., Pei, J., Vergara, I.A., Nesbitt, M., Wang, K., and Chen, N. 2008. OrthoCluster: A new tool for mining synteny blocks and applications in comparative genomics. In 11th International Conference on Extending Technology (EDBT), March 25‐30, 2008, Nantes, France.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library