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Using the Generic Genome Browser (GBrowse)
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Unit 9.9
DOI:
10.1002/0471250953.bi0909s28
Online Posting Date:
December, 2009 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
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
Figures
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Figure 9.9.1Example features from the volvox1.gff file as displayed with the volvox.conf configuration file. -
Figure 9.9.2The first few lines of the genome “features” from the volvox1.gff file. -
Figure 9.9.3Display of the feature using the primers glyph. -
Figure 9.9.4An excerpt from the example file volvox2.gff is shown here. -
Figure 9.9.5The GBrowse details view displaying the Note attribute from the GFF file. -
Figure 9.9.6The data file volvox3.gff contains a simulated dataset of a series of gapped nucleotide alignments. An excerpt from the file is shown here. -
Figure 9.9.7Multi-segmented features are not properly displayed unless the appropriate aggregator is activated in the configuration file. -
Figure 9.9.8Turning on the match aggregator in the configuration file displays the match feature with its subparts correctly. -
Figure 9.9.9The contents of the file volvox4.gff. -
Figure 9.9.10An image of the canonical processed_transcript glyph. -
Figure 9.9.11Image of a UCSC Genome Browser look-alike processed_transcript glyph. -
Figure 9.9.12The cds glyph shows the reading frame using a musical staff notation. -
Figure 9.9.13GBrowse detailed view with default viewing options for yeast genome. -
Figure 9.9.14Initial page view for the yeast_chr1 sample database installed with GBrowse. -
Figure 9.9.15Detailed view for the Nut21 link from yeast_chr1 database.
Literature Cited
| 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 | |
| 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. | |
| dradians.conf | |
| Configuration file for use with | |
Supplemental Files
Listed below are sample data files for this Unit. Right click on the file names and select the "Save target as" or "Save link as" option to save the file to your computer.
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