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User:Girlwithglasses/Template:ToolData/gbrowse

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{{ {{{template}}} | name = GBrowse | status = mature | dev = maintenance | support = active | os_web = yes | os_mac = yes | os_linux = yes | os_win = yes | os_unix = yes | logo = GBrowseLogo.png | home = http://gbrowse.org | note = 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. | about = 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)
| scrnsht =

| dl = http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ | dl_src = http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/ | dl_dev = GBrowse repository on GitHub | getting_started_preamble = | req = 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. | install = GBrowse 2.x installation guide | config = Configuration guide | doc =

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:

| papers = publications

  • 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 = interactive tutorials or workshops | presentations = non-interactive tutorials or workshops | mail =

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

| logo_info = 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. | wild_urls =

| dev_ppl = who is developing the tool? | dev_status = what's going on at the moment | tool_type = tool type / features

  • Community Annotation
  • Comparative Genome Visualization
  • Database schema
  • Database (Chado) web front ends
  • Database tools
  • Gene Expression Visualization
  • Genome Annotation
  • Genome Visualization & Editing
  • Literature Tools
  • Middleware
  • Molecular Pathway Visualization
  • Ontology Visualization
  • Sequence Alignment
  • Tool Integration
  • Workflow Management

| formats = }}
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