Difference between revisions of "GBrowse syn Help"
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− | + | [[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. | |
− | + | ||
− | [[ | + | |
− | ==Display Settings== | + | =Search Section= |
− | ===Image | + | [[Image:GBS_Search_Section.png|border]] |
− | ===Image | + | |
+ | ==Landmark== | ||
+ | [[Image:GBS_Landmark.png|border]] | ||
+ | *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== | ||
+ | [[Image:GBS_ref_Species.png|border]] | ||
+ | * 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== | ||
+ | [[Image:GBS_aln_Species.png|border]] | ||
+ | * 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== | ||
+ | [[Image:GBS_Datasource.png|border]] | ||
+ | *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== | ||
+ | [[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. | ||
+ | ** 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 | ||
+ | [[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. | ||
+ | |||
+ | ==Image Options== | ||
+ | ===Chain Alignments=== | ||
+ | [[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"> | ||
+ | |||
+ | ===Flip Minus Strand Panels=== | ||
+ | [[Image:GBS_flip.png|border]] | ||
+ | * 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. | ||
+ | [[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]] |
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.
Contents
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 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 Settings
Image Widths
- the total width of the displayed reference sequence panel.
Image Options
Chain Alignments
- 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.
Flip Minus Strand Panels
- 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.
Grid Lines
- 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.
Edges
- This option is on by default, it outlines the polygons that connect aligned blocks
Shading