GBrowse syn Help

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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

GBS Search Section.png

Landmark

GBS Landmark.png

  • 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

GBS ref Species.png

  • 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

GBS aln Species.png

  • 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

GBS Datasource.png

  • 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

GBS Display Mode1.png   GBS Display Mode2.png

  • The default display mode shows the reference species plus two aligned species per panel and repeats the display panel as many times as required to display all aligned species relative to the reference species.
    • This mode is best suited to displaying all sequences on roughly the same scale.
  • The other display mode is a summary view that shows all species in a single panel.


Display mode: All species on a single panel



Display mode: Refence species plus two aligned species/panel
  • 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

GBS Display Settings.png

Image widths

Image options