User:Girlwithglasses/Template:ToolData/gbrowse syn

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{{ {{{template}}} | name = GBrowse_syn | status = mature | dev = active? | support = active | os_web = yes | os_mac = yes | os_linux = yes | os_win = yes | os_unix = yes | 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).

| scrnsht =
GBrowse_syn, as implemented at WormBase

| public_server = | dl = | dl_src = | dl_dev = | 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 mutliple sequence alignments.

More information on GBrowse_syn configuration

| usage = 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.

| doc = | papers = Please refer to the following paper when citing GBrowse_syn:

| tutorials =

| presentations =

| 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. | wild_urls =

| dev_ppl = | dev_status = See the discussion page for notes on further GBrowse_syn development. | tool_type =

  • Comparative Genome Visualization

| formats = | 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:

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