Genome viewer

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General organization[edit]

The genome viewer can be accessed through many pages on the Listeriomics website. From the home webpage, from the transcriptomics and proteomics summary pages, from the gene tool webpage, and from the small RNA tool webpage.

Printscreen of the Genome viewer of the Listeriomics website
Control panel
  • Add data
  • Move the genome position, zoom in, zoom out
  • Manage displayed datasets

Omics data viewer

The panel in which "omics" datasets are displayed

Genome annotation

All genome features available for the displayed Listeria strain genome.

Mouse interactions

  • Left-click on the omics data viewer will display a vertical line indicating the genome position in base pair (bp).
  • Left-click on the genome annotation panel will display more information on the selected genome feature.
  • Right-click on the genome annotation panel will center the view.
  • Double-click on the genome annotation panel will open the corresponding gene or small RNA webpage.

Control panel[edit]

Control panel of the genome viewer

Dialog window for adding data to genome viewer
Add data

Two buttons are available to add datasets, one for transcriptomic data, the other for proteomic. Both will open a similar dialog with all datasets available. The user can filter datasets or directly search them. Every dataset selected will be displayed on the genome viewer by clicking on the Ok button.

Printscreen of the same region with different base pair scale
Change view
  • Scroll the genome by searching a specific element contained in the displayed Listeria strain genome.
  • Zoom in and zoom out horizontally, to change the base pair scale of display.
  • AT button gives instant access to a view at the sequence scale where DNA sequence is displayed, along with amino acid sequence in the 6 possible frames.
  • Increase the height of all genome tracks.
Dialog window for managing data and getting the legend for the genome viewer
Manage data

There are 4 different buttons in this panel:

  • Access the dialog window to look at the data legend and remove specific datasets from the view
  • Save in text file the current genome viewer properties
  • Change the display between absolute expression value (Log(expression)) to relative expression value (Log(Fold Change)). Thus, the user can switch from displaying biological condition absolute expression datasets to comparisons of biological conditions relative datasets.
  • Select one of the three representation types: Display by biological condition, by dataset, or overlap all datasets on one single track.

Omics data viewer[edit]

Omics data viewer of the genome viewer
The genome viewer will always display "omics" dataset in that order:
  • RNASeq data
  • Tiling array
  • Gene expression array
  • Transcription Start Site (TSS) data
  • Proteomic data:

For each track the name of the dataset displayed is shown on the top left. The grey line in the middle of each track is the value 0. If the name of the dataset contains "vs" it means it is a relative expression dataset, thus Log(Fold Change) values are displayed. The type of data displayed is written at the end of each dataset name on the top left of each track.

  • Move view vertically:

When the height of the view has been increased or decrease using the Height zoom the vertical slider will be used to move from one dataset to the other.

Genome annotation[edit]

Genome annotation panel of the genome viewer

It shows the position in base pair (bp) in the Listeria strain genome, and all the genome features available with a fix color code. There is an horizontal bar to browse the genome.

Genome feature color legend of the genome viewer
All the genome features available are displayed here with their color code.