Using the Generic Genome Browser (GBrowse)
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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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PDF or HTML at Wiley Online LibraryTable 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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Figure 9.9.1 Example features from the volvox1.gff file as displayed with the volvox.conf configuration file. View Image -
Figure 9.9.2 The first few lines of the genome “features” from the volvox1.gff file. View Image -
Figure 9.9.3 Display of the feature using the primers glyph. View Image -
Figure 9.9.4 An excerpt from the example file volvox2.gff is shown here. View Image -
Figure 9.9.5 The GBrowse details view displaying the Note attribute from the GFF file. View Image -
Figure 9.9.6 The data file volvox3.gff contains a simulated dataset of a series of gapped nucleotide alignments. An excerpt from the file is shown here. View Image -
Figure 9.9.7 Multi‐segmented features are not properly displayed unless the appropriate aggregator is activated in the configuration file. View Image -
Figure 9.9.8 Turning on the match aggregator in the configuration file displays the match feature with its subparts correctly. View Image -
Figure 9.9.9 The contents of the file volvox4.gff. View Image -
Figure 9.9.10 An image of the canonical processed_transcript glyph. View Image -
Figure 9.9.11 Image of a UCSC Genome Browser look‐alike processed_transcript glyph. View Image -
Figure 9.9.12 The cds glyph shows the reading frame using a musical staff notation. View Image -
Figure 9.9.13 GBrowse detailed view with default viewing options for yeast genome. View Image -
Figure 9.9.14 Initial page view for the yeast_chr1 sample database installed with GBrowse. View Image -
Figure 9.9.15 Detailed view for the Nut21 link from yeast_chr1 database. View Image
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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