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GBrowse syn/tool data

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{{ {{{template}}} | name = GBrowse_syn | full_name = Generic Synteny Browser | status = beta release | dev = active | support = active | type = Comparative genome visualization | platform = web | logo = GBrowse_syn_logo.png | home = | about = GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It can be used to view multiple sequence alignment data, synteny or co-linearity data from other sources against genome annotations provided by GBrowse. GBrowse_syn is included with the standard GBrowse package (version 1.69 and later).

| screenshot =
GBrowse_syn, as implemented at WormBase

| public_server = | dl = | dl_url = https://github.com/GMOD/GBrowse | dl_src = | dl_src_url = | dl_dev = | dl_dev_url = https://github.com/GMOD/GBrowse | getting_started_preamble = GBrowse_syn has been part of the GBrowse distribution since version 1.69; we recommend using the most up-to-date version of GBrowse 2. Please follow the installation instructions for GBrowse. | req = | install = | config = Configuration of GBrowse_syn is much the same as for GBrowse, with database and display options controlled by a configuration file. GBrowse_syn uses a main configuration file for general options plus an individual configuration for each species represented in the multiple sequence alignments.

More information on GBrowse_syn configuration | doc = See the help for GBrowse_syn

Alignment data

  • GBrowse_syn uses a central 'joining' database that contains information about the multiple sequence alignments
  • There is an additional GBrowse database for each species represented in the alignments
  • The databases for each species are configured in the same way as a regular GBrowse installations
  • Details on the GBrowse_syn database

User interface

The overall look of Gbrowse_syn resembles GBrowse but has some key differences to accomodate the more complex comparative genome data (see the screenshot above).

GBrowse_syn uses a central "reference species" panel, with inset panels above and below for two or more aligned species. There is no upper limit to the number of species that can be displayed. | papers = Please refer to the following paper when citing GBrowse_syn:

  • Using the Generic Synteny Browser (GBrowse_syn) [1]

| presentations = * Challenges in Comparative Genome Browsing - Presented by Sheldon McKay at the European Bioinformatics Institute, Hinxton, UK.

| tutorials =

GBrowse syn Tutorial
Installing and configuring GBrowse_syn; from the 2013 GMOD Summer School

| wild_urls = *The Arabidopsis Information Resource

| mail = Support is via the GBrowse mailing list:

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_syn logo was created by Darek Lakey, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College. | dev_ppl = | dev_status = See the discussion page for notes on further GBrowse_syn development. | contact_email = Sheldon Mckay | input = | output = | see_also = The focus of this documentation is the GBrowse_syn application. However, the generation of whole genome alignments and identification of orthologous regions are the subject of considerable interest, so some background reading is listed below:

| demo_server = http://mckay.cshl.edu/cgi-bin/gbrowse_syn/mercator/?search_src=Cbri;name=chrX:620000..670000 | survey_link = GBrowse_syn |release date=2007 | extras =

Included in

Cloud component

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