Using the Generic Genome Browser (GBrowse)

Maureen J. Donlin1

1 Department of Biochemistry and Molecular Biology and Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 9.9
DOI:  10.1002/0471250953.bi0909s28
Online Posting Date:  December, 2009
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Abstract

A genome browser is software that allows users to visualize DNA, protein, or other sequence features within the context of a reference sequence, such as a chromosome or contig. The Generic Genome Browser (GBrowse) is an open‐source browser developed as part of the Generic Model Organism Database project (Stein et al., 2002). GBrowse can be configured to display genomic sequence features for any organism and is the browser used for the model organisms Drosophila melanogaster (Grumbling and Strelets, 2006) and Caenorhabditis elegans (Schwarz et al., 2006), among others. The software package can be downloaded from the Web and run on a Windows, Mac OS X, or Unix‐type system. Version 1.64, as described in the original protocol, was released in November 2005, but the software is under active development and new versions are released about every six months. This update includes instructions on updating existing data sources with new files from NCBI. Curr. Protoc. Bioinform. 28:9.9.1‐9.9.25. © 2009 by John Wiley & Sons, Inc.

Keywords: computational biology; genome; GBrowse; genome browser

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Configuration and Use of GBrowse 1.X
  • Basic Protocol 2: Setting Up a MySQL‐Based GBrowse
  • Support Protocol 1: Installing GBrowse in the Unix/Linux Environment
  • Support Protocol 2: Setting Up a Database from NCBI Genbank Files
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Furey, T.S. 2006. Comparison of human (and other) genome browsers. Hum. Genomics 2:266‐270.
   Grumbling, G. and Strelets, V. 2006. FlyBase: Anatomical data, images and queries. Nucleic Acids Res. 34:D484‐D488.
   Lewis, S.E., Searle, S.M., Harris, N., Gibson, M., Lyer, V., Richter, J., Wiel, C., Bayraktaroglir, L., Birney, E., Crosby, M.A., Kaminker, J.S., Matthews, B.B., Prochnik, S.E., Smithy, C.D., Tupy, J.L., Rubin, G.M., Misra, S., Mungall, C.J., and Clamp, M.E. 2002. Apollo: A sequence annotation editor. Genome Biol. 3:0082.1‐0082.14.
   Schwarz, E.M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Canaran, P., Chan, J., Chen, N., Chen, W.J., Davis, P., Fiedler, T.J., Girard, L., Harris, T.W., Kenny, E.E., Kishore, R., Lawson, D., Lee, R., Muller, H.M., Nakamura, C., Ozersky, P., Petcherski, A., Rogers, A., Spooner, W., Tuli, M.A., Van Auken, K., Wang, D., Durbin, R., Spieth, J., Stein, L.D., and Sternberg, P.W. 2006. WormBase: Better software, richer content. Nucleic Acids Res. 34:D475‐D478.
   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.
Key Reference
   Stein et al., 2002. See above.
  This article gives extensive background and descriptive details on how and why the Generic Genome Browse was developed.
Internet Resources
  http://gmod.org/wiki/Main_Page
  Generic Model Organism Database (GMOD): Tutorials, overviews, and links for downloading GBrowse.
  https://lists.sourceforge.net/lists/listinfo/gmod‐gbrowse
  GMOD‐GBrowse mailing list: Join the mailing list to ask questions about installation and use of GBrowse and to be notified of new releases.
  http://gmod.org/wiki/GBrowse_2.0_HOWTO
  GBrowse 2.0 HOWTO: This site provides instructions on installing and configuring GBrowse 2. There are links to HOWTOs on migrating from GBrowse 1.X to 2.
  http://www.nabble.com/gmod‐gbrowse‐f3500.html
  Nabble: Search engine for various internet forums, including GMOD‐Gbrowse
  http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
  General Feature Format (GFF) specification: Get detailed information about the GFF and download scripts for converting various computational analyses to GFF format.
Supplemental File
  Supplemental files can be downloaded from http://www.currentprotocols.com/protocol/bi0909 by clicking the Supplemental Files tab and selecting the needed file.
  Configuration file for use with . This file is an edited version of 08.genbank.conf file that is installed with the gbrowse package.
  dradians.conf
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