GenomeView

From CoGepedia

NOTE: This page is out of date and does not reflect recent migration to the JBrowse viewer.  We will update it soon!

Contents

Navigation

Panning left-right

There are several ways to move along a genomic region:

  • Click on the chromosome and drag with mouse
  • Use the left/right arrows located on the left of the viewer
  • Use scroll bar below graphics by clicking and dragging, or clicking somewhere in the bar

Zooming in and out

You can zoom into and out of a genomic region by:

  • Using navigation menu on the left of the viewer. (+) zooms in, (-) zooms out, and the tick-marks take you a specific zoom level.
  • Double-clicking on a region will zoom in one level
  • Use the mouse scroll-wheel to zoom in and out if the mouse pointer is over the chromosome

Changing displayed information

There are often many types of genomic information that can be displayed as overlays. To toggle various overlays, open the overlay menu by clicking on the "+" symbol in the top right corner of the viewer and select the overlays you wish to view.

Getting additional information and data

GenomeView has several ways to get information:

Annotations

  • Full Genomic Feature Annotations: Simply click on a feature, and a window will appear with the complete annotation for all features at that location. This window is resizeable and draggable. Please see Annotation information, for more information about the information and links provided in this view.
  • Popup-annotations: Select the "Pop-up Annotations" in the lower right hand part of the navigation screen, and the names of genomic features will pop-up when the mouse pointer hovers over them for a second. This window is resizable and draggable.
  • Genome Information: Click on the "Genome Info" button in the lower left hand part of the navigation screen and an overview of the genome will pop-up.

Note: many of the annotations contain links to other parts of CoGe. For example, if you want to get the sequence of a feature, just click on its location information in the pop-up annotation window.

Grab Sequence

To get genomic sequence in fasta format:
  1. Click "Grab Sequence" button in lower left of navigation screen.
  2. Click two regions in the genomic view to set the start and stop positions of the sequence you wish to grab.
  3. Click "View Sequence" to launch SeqView and get the sequence of the selected region in fasta format.

Extract Genomic Features

To genomic features:
  1. Click "Extract Features" button in lower left of navigation screen.
  2. Click two regions in the genomic view to set the start and stop positions of the sequence you wish to grab.
  3. Click "Get Features" to launch FeatList and get a list of all genomic features in the selected region.

Understanding the image

CoGe's genomic visualization library, GeLo, permits the creation of a virtual chromosome using any style of glyphs to represent genomic information. Below are the common implementations used in CoGe

Genomic Features

Genomic features are usually drawn as arrows or blocks of varying size and color. While there is some variation in how such features are drawn due to difference in how they were specified in the original data source (e.g. do mRNAs include introns?), the general conventions used in CoGe are:

  • Grey (narrow): Gene. Usually starting at the beginning of the transcript, stopping at the end of the transcript, and including all intronic sequence, if appropriate.
  • blue: mRNA transcript
  • Green: CDS/protein coding regions (Please see note below)
  • grey (large): RNA gene (tRNA, rRNA, etc.)
  • orange-red: pseudogene

Note: There are options in CoGe to color protein coding regions (CDS) based on the GC content of the wobble position in the codon. If this visualization is use, a color gradient is used to depict the wobble GC content such that:

  • red: AT rich in CDS wobble positions
  • green: GC rich in CDS wobble positions
  • yellow: 50%/50% AT/GC in CDS wobble positions

Background of virtual chromosome

The background of a genomic image can also be colored. Most often, this is used to color the genomic GC content such that:

  • green: GC rich
  • white: AT rich
  • orange: Unsequenced (N)
  • purple: masked sequenced (X). Masked genomes are generated often to remove repetitive sequence.

Expanding overlapping genomic features

When genomic features overlap, as happens with alternatively spliced transcripts, you often have the option of drawn these on top of one another, or have CoGe detect this and drawn them above and below one another.

  • Select "Expand Overlapping Gene Models" in the lower right of the screen to turn this on

Examples and descriptions of GenomeView's visualization

As there are many different types of visualization, please follow this link: GenomeView examples.

Other options

Flat Gene Models

Flat gene models are simple arrows without the "tubular" design. This was the original way gene models were drawn before Josh Kane updated the model.

Expand Gene Models

Separates genomic features that overlap at the same genomic position. Usually happens when alternatively spliced transcripts are annotated.

Save Settings

Registered users can save which information they want to see by default as well as how gene models are drawn"

Window Width

Sets the size of the window used for navigating a genomic region. Options in the top-left of navigation window

  • Resize: sets the navigation window to the size specified in the "Window Width" box (in pixels)
  • Full Screen: sets the navigation window to the size of the browser window

Linking to GenomeView

See Linking to GenomeView for information on how to link to GenomeView.



Examples

Identifying Horizontal Gene Transfer using GC content in wobble position coloring

Horizontal Gene Transfer