GBrowse

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GBrowse logo
Status
  • Mature release
  • Development: active
  • Support: active
Licence
{{{PAGENAME}}} is open source

GPL 2.0, Artistic License 2.0

Resources


About Generic Genome Browser (GBrowse)

GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:

  • Simultaneous bird's eye and detailed views of the genome.
  • Scroll, zoom, center.
  • Use a variety of premade glyphs or create your own.
  • Attach arbitrary URLs to any annotation.
  • Order and appearance of tracks are customizable by administrator and end-user.
  • Search by annotation ID, name, or comment.
  • Supports third party annotation using GFF formats.
  • Settings persist across sessions.
  • DNA and GFF dumps.
  • Connectivity to different databases, including BioSQL and Chado.
  • Multi-language support.
  • Third-party feature loading.
  • Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features)

Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used.


Visit the GBrowse website.

Screenshots

Downloads

GBrowse can also be found on CPAN and in the Debian sid ("unstable") apt package repository and can be installed via apt-get in Ubuntu 12.04 and later.

Using GBrowse

System Requirements

GBrowse is Perl-based and the GBrowse 2.x modules are hosted on CPAN. GBrowse can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed.

Installation

Configuration

Documentation

POD documentation

There are many useful POD documents included with the distribution. These are converted to HTML files when you install the package, and can be found in /gbrowse/docs/pod.

GBrowse 2.x pod documents can also be viewed online at CPAN:

Installation

Configuration

Documentation

POD documentation

There are many useful POD documents included with the distribution. These are converted to HTML files when you install the package, and can be found in /gbrowse/docs/pod.

GBrowse 2.x pod documents can also be viewed online at CPAN:

Publications, Tutorials, and Presentations

Publications on or mentioning GBrowse

  • Using the Generic Genome Browser (GBrowse). [1]
  • SNP@Evolution: a hierarchical database of positive selection on the human genome. [2] (GBrowse-related)
  • TBrowse: an integrative genomics map of Mycobacterium tuberculosis. [3] (GBrowse-related)
  • FishMap: a community resource for zebrafish genomics. [4] (GBrowse-related)
  • Using the Generic Genome Browser (GBrowse). [5]
  • Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. [6] (See YSB.)
  • Gbrowse Moby: a Web-based browser for BioMoby Services. [7]
  • The generic genome browser (GBrowse): a building block for a model organism system database. [8] PDF

Tutorials

GBrowse tutorial from 2012 GMOD Summer School. This relies heavily on the GBrowse2 Admin Tutorial.
Demonstrates setting up, configuring and using GBrowse with some sample data. GBrowse is provided on an Amazon Machine Image; see GMOD in the Cloud for more information on getting a GMOD AMI.
GBrowse tutorial from 2010 GMOD Summer School
Set up and run GBrowse with sample data. It provides a VMware image to work on, and relies heavily on the GBrowse2 Admin Tutorial.
GBrowse2 Admin Tutorial
Step by step guide on how to configure and load data into GBrowse. Administration tutorials are available for both the GBrowse2 Admin Tutorial, and the earlier 1.x versions.
Usage tutorial
GBrowse usage tutorial
GBrowse NGS Tutorial
Instructions on how to visualize next generation sequencing data in GBrowse using SAMtools. The tutorial includes a starting VMware image, and uses the example data that comes with SAMtools.
GBrowse video tutorial
Produced by EuPathDB; please direct praise and thanks to them!
GBrowse User Tutorial at OpenHelix
A Flash based tutorial on using GBrowse. Provided by OpenHelix. Tutorial includes slides, handouts and exercises. NB: this tutorial is for GBrowse 1.x


Contacts and Mailing Lists

Mailing List Link Description Archive(s)
GBrowse & GBrowse_syn gmod-gbrowse GBrowse and GBrowse_syn users and developers. Gmane, Nabble (2010/05+), Sourceforge
gmod-gbrowse-cmts Code updates. Sourceforge
Please report bugs to the Bug Tracker (select 'Category: Gbrowse').

GBrowse in the wild

Public installations of GBrowse:



See also

JBrowse, the successor to GBrowse, built with JavaScript for a faster, more interactive user experience; and WebGBrowse, a tool for configuring GBrowse.

More on GBrowse

See Category:GBrowse

The GBrowse logo was created by Alex Read, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.

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Facts about "GBrowse"RDF feed
Available on platformweb +
Date published2009 +, 2008 +, 2007 +, 2006 + and 2002 +
Has DOI10.1002/0471250953.bi0909s28 +, 10.1186/1471-2148-9-221 +, 10.1016/j.tube.2009.07.005 +, 10.1089/zeb.2008.0531 +, 10.1002/0471250953.bi0909s17 +, 10.1371/journal.pone.0000322 +, 10.1186/1751-0473-1-4 + and 10.1101/gr.403602 +
Has PMCIDPMC2755008 +, PMC1829191 +, PMC1636335 + and PMC187535 +
Has PMID19957275 +, 19732458 +, 19683474 +, 18554176 +, 18428797 +, 17389913 +, 17147784 + and 12368253 +
Has URLhttp://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ +, https://github.com/GMOD/GBrowse +, http://gbrowse.org +, http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ +, http://flybase.org/cgi-bin/gbrowse/dmel + and http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse +
Has authorDonlin MJ +, Cheng F +, Chen W +, Richards E +, Deng L +, Zeng C +, Bhardwaj A +, Bhartiya D +, Kumar N +, Open Source Drug Discovery Consortium +, Scaria V +, Meli R +, Prasad A +, Patowary A +, Lalwani MK +, Maini J +, Sharma M +, Singh AR +, Kumar G +, Jadhav V +, Sivasubbu S +, Schacherer J +, Ruderfer DM +, Gresham D +, Dolinski K +, Botstein D +, Kruglyak L +, Wilkinson M +, Stein LD +, Mungall C +, Shu S +, Caudy M +, Mangone M +, Day A +, Nickerson E +, Stajich JE +, Harris TW +, Arva A + and Lewis S +
Has descriptionGBrowse is a combination of database and iGBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:
  • Simultaneous bird's eye and detailed views of the genome.
  • Scroll, zoom, center.
  • Use a variety of premade glyphs or create your own.
  • Attach arbitrary URLs to any annotation.
  • Order and appearance of tracks are customizable by administrator and end-user.
  • Search by annotation ID, name, or comment.
  • Supports third party annotation using GFF formats.
  • Settings persist across sessions.
  • DNA and GFF dumps.
  • Connectivity to different databases, including BioSQL and Chado.
  • Multi-language support.
  • Third-party feature loading.
  • Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, find oligonucleotides, design primers, create restriction maps, edit features)
Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used.
is required and a single database is used. +
Has development statusactive +
Has full nameGeneric Genome Browser +
Has input formatGFF3 + and GFF2 +
Has licenceGPL2 + and Artistic License +
Has logoGBrowseLogo.png +
Has publication detailsCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 9: Unit 9.9 +, BMC evolutionary biology 9: 221 +, Tuberculosis (Edinburgh, Scotland) 89: 386-7 +, Zebrafish 5: 125-30 +, PloS one 2: e322 +, Source code for biology and medicine 1: 4 + and Genome research 12: 1599-610 +
Has software maturity statusmature +
Has support statusactive +
Has titleWormBase +, FlyBase +, HapMap +, Using the Generic Genome Browser (GBrowse). +, SNP@Evolution: a hierarchical database of positive selection on the human genome. +, TBrowse: an integrative genomics map of Mycobacterium tuberculosis. +, FishMap: a community resource for zebrafish genomics. +, Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. +, Gbrowse Moby: a Web-based browser for BioMoby Services. + and The generic genome browser: a building block for a model organism system database. +
Has topicGBrowse +
Is open sourceYes +
Link typedownload +, source code +, website + and wild URL +
Published inCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] +, BMC evolutionary biology +, Tuberculosis (Edinburgh, Scotland) +, Zebrafish +, PloS one +, Source code for biology and medicine + and Genome research +
Release date1 January 2001 +
Tool functionality or classificationGenome Visualization & Editing +
Written in languagePerl +
Has subobjectThis property is a special property in this wiki.GBrowse#http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ +, GBrowse#https://github.com/GMOD/GBrowse +, GBrowse#http://gbrowse.org +, GBrowse#http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ +, GBrowse#http://flybase.org/cgi-bin/gbrowse/dmel + and GBrowse#http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/gbrowse +