Difference between revisions of "GBrowse syn Help"

From GMOD
Jump to: navigation, search
(Display Mode)
(Grid Lines)
 
(32 intermediate revisions by the same user not shown)
Line 1: Line 1:
=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.
 
[[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==
+
=Search Section=
 
[[Image:GBS_Search_Section.png|border]]
 
[[Image:GBS_Search_Section.png|border]]
  
===Landmark===
+
==Landmark==
 
[[Image:GBS_Landmark.png|border]]
 
[[Image:GBS_Landmark.png|border]]
 
*The landmark input box accepts segment labels in the form:
 
*The landmark input box accepts segment labels in the form:
Line 15: Line 13:
 
* Note, make sure you have selected the correct reference species before clicking the 'Search' button.
 
* Note, make sure you have selected the correct reference species before clicking the 'Search' button.
  
===Reference Species===
+
==Reference Species==
 
[[Image:GBS_ref_Species.png|border]]
 
[[Image:GBS_ref_Species.png|border]]
 
* This is the species that occupies the center panel in the alignment display.
 
* This is the species that occupies the center panel in the alignment display.
Line 21: Line 19:
 
* Select the species from the pull-down menu and check boxes (see below) to select which species should be aligned to the reference sequence.
 
* 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===
+
==Aligned Species==
 
[[Image:GBS_aln_Species.png|border]]
 
[[Image:GBS_aln_Species.png|border]]
 
* Configured species (except for the reference species) for the selected data source will be listed here.
 
* 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.
 
* By checking each box, you indicate that alignments for this species, if available, should be displayed relative to the reference species.
  
===Data Source===
+
==Data Source==
 
[[Image:GBS_Datasource.png|border]]
 
[[Image:GBS_Datasource.png|border]]
 
*This pull-down menu lists all available data sets configured for the synteny browser.
 
*This pull-down menu lists all available data sets configured for the synteny browser.
Line 32: Line 30:
 
*If only one data source is available this menu will not appear.
 
*If only one data source is available this menu will not appear.
  
===Display Mode===
+
==Display Mode==
 
[[Image:GBS_Display_Mode1.png|border]]   [[Image:GBS_Display_Mode2.png|border]]
 
[[Image:GBS_Display_Mode1.png|border]]   [[Image:GBS_Display_Mode2.png|border]]
 
*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.
 
*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.
 
** 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.
 
* The other display mode is a summary view that shows all species in a single panel.
<br>
+
* 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
[[Image:GBS_compact.png|border|800px|left|thumb|bla bla bla]]
+
[[Image:GBS_expanded.png|border|800px|left|thumb|Display mode: Refence species plus two aligned species/panel; repaeted until all aligned species are shown]]
 +
[[Image:GBS_compact.png|border|800px|left|thumb|Display mode: All species on a single panel]]
 +
<br clear=all>
  
 +
=Display Settings=
 +
[[Image:GBS_Display_Settings.png|border|800px]]
 +
==Image Widths==
 +
[[Image:GBS_widths.png|border]]
 +
* the total width of the displayed reference sequence panel.
  
<br>
+
==Image Options==
[[Image:GBS_expanded.png|border|800px|left]]
+
===Chain Alignments===
*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
+
[[Image:GBS_chain.png|border]]
 +
* GBrowse_syn uses a dynamic programming algorithm to assembled aligned regions into chains.
 +
** If alignments are on the same strand on the same reference sequence and their coordinates increase (or decrease) monotonically, they are assembled into a meta-alignment, which is indicated by dashed connectors.
 +
** Chained alignments may have other alignments in the intervening gaps.
 +
* This feature is useful for displaying small rearrangements, such as translocations, nested inversions, etc.
 +
[[Image:GBS_chained.png|border|800px|thumb|Chained aligments|left]]
 +
<br clear="all">
 +
[[Image:GBS_nochain.png|border]]
 +
[[Image:GBS_unchained.png|border|800px|thumb|Unchained aligments|left]]
 +
<br clear="all">
  
==Display Settings==
+
===Flip Minus Strand Panels===
[[Image:GBS_Display_Settings.png|border|800px]]
+
[[Image:GBS_flip.png|border]]
===Image widths===
+
* Choosing the flip option makes it easier directly compare the aligned regions.
===Image options===
+
* Otherwise, in alignments is on the negative strand, relative to the reference, the grid lines and shaded polygon will cross-over to indicate inversion
 +
* Unless the flip option is turned off, the decision to flip a panel is determined by the number of (+) vs (-) aligned base pairs.
 +
[[Image:GBS_flipped.png|border|800px|thumb|Reverse strand panel (''C. briggsae'') flipped to facilitate direct comparison of gene order|left]]
 +
[[Image:GBS_unflipped.png|border|800px|thumb|Reverse strand panel keo in original orientation|left]]
 +
<br clear="all">
 +
 
 +
===Grid Lines===
 +
[[Image:GBS_lines.png|border]]
 +
* Grid lines use insertion/deletion data from the multiple sequence alignments to provide a visual representation of sequence loss or gain
 +
* This feature is useful because it provides fine-grained information about the underlying sequence changes within aligned regions.
 +
* Every fifth line is thicker to provide a visual cue help trace the lines between species.
 +
 
 +
[[Image:GBS_noglines.png|border|800px|thumb|Alignment of ''C. elegans'' and ''C. remanei'', showing the R193.2 gene|left]]
 +
[[Image:GBS_glines.png|border|800px|thumb|The same alignment with grid-lines turned on.  Note the large gain/loss of intron sequence|left]]
 +
<br clear="all">
 +
 
 +
===Edges===
 +
[[Image:GBS_edges.png|border]]
 +
* This option is on by default, it outlines the polygons that connect aligned blocks
 +
 
 +
[[Image:GBS_edgeson.png|border|800px|thumb|An alignment view with edges on grid-lines and shading off|left]]
 +
<br clear="all">
 +
 
 +
===Shading===
 +
[[Image:GBS_shading.png|border]]
 +
 
 +
[[Image:GBS_shadingon.png|border|800px|thumb|An alignment view with shading on and grid-lines and edges off|left]]
 +
<br clear="all">
  
 
[[Category:GBrowse syn]]
 
[[Category:GBrowse syn]]

Latest revision as of 12:40, 22 August 2009

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.
  • 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 mode: Refence species plus two aligned species/panel; repaeted until all aligned species are shown
Display mode: All species on a single panel


Display Settings

GBS Display Settings.png

Image Widths

GBS widths.png

  • the total width of the displayed reference sequence panel.

Image Options

Chain Alignments

GBS chain.png

  • GBrowse_syn uses a dynamic programming algorithm to assembled aligned regions into chains.
    • If alignments are on the same strand on the same reference sequence and their coordinates increase (or decrease) monotonically, they are assembled into a meta-alignment, which is indicated by dashed connectors.
    • Chained alignments may have other alignments in the intervening gaps.
  • This feature is useful for displaying small rearrangements, such as translocations, nested inversions, etc.
Chained aligments


GBS nochain.png

Unchained aligments


Flip Minus Strand Panels

GBS flip.png

  • Choosing the flip option makes it easier directly compare the aligned regions.
  • Otherwise, in alignments is on the negative strand, relative to the reference, the grid lines and shaded polygon will cross-over to indicate inversion
  • Unless the flip option is turned off, the decision to flip a panel is determined by the number of (+) vs (-) aligned base pairs.
Reverse strand panel (C. briggsae) flipped to facilitate direct comparison of gene order
Reverse strand panel keo in original orientation


Grid Lines

GBS lines.png

  • Grid lines use insertion/deletion data from the multiple sequence alignments to provide a visual representation of sequence loss or gain
  • This feature is useful because it provides fine-grained information about the underlying sequence changes within aligned regions.
  • Every fifth line is thicker to provide a visual cue help trace the lines between species.
Alignment of C. elegans and C. remanei, showing the R193.2 gene
The same alignment with grid-lines turned on. Note the large gain/loss of intron sequence


Edges

GBS edges.png

  • This option is on by default, it outlines the polygons that connect aligned blocks
An alignment view with edges on grid-lines and shading off


Shading

GBS shading.png

An alignment view with shading on and grid-lines and edges off