GBrowse syn Help

GBrowse_syn User Interface Help

GBrowse_syn is a GBrowse based synteny viewer. This page provides help on using GBrowse_syn. See the GBrowse_syn page for other information on GBrowse_syn.

Search Section

Landmark

• The landmark input box accepts segment labels in the form:

reference sequence:start..end

• In some cases, gene names and other landmarks can also be entered. Support for searching other classes depends on the configuration for the species' data source.
• Note, make sure you have selected the correct reference species before clicking the 'Search' button.

Reference Species

• This is the species that occupies the center panel in the alignment display.
• Alignments for other species are shown with reference to this coordinate system.
• Select the species from the pull-down menu and check boxes (see below) to select which species should be aligned to the reference sequence.

Aligned Species

• Configured species (except for the reference species) for the selected data source will be listed here.
• By checking each box, you indicate that alignments for this species, if available, should be displayed relative to the reference species.

Data Source

• This pull-down menu lists all available data sets configured for the synteny browser.
• Each item in this list corresponds to a sourcename.synconf configuration file.
• If only one data source is available this menu will not appear.

Display Mode

   

• The default display mode is to have the refernce species plus two aligned species per panel.
  • This mode is best suited to displaying all sequences on roughly the same scale.
• The other display mode is

• The display mode can be toggled between expanded and compact by clicking the link shown above or via a pull-down menu on the "Display Settings" section

Display Settings