hfv top banner
HFV Ebola sequence database
 

Ebola Genome Browser Help

This genome browser is a customization of JBrowse, built to incorporate multiple sources of information about Ebolavirus.

Nucleotide views can include:

Protein views can include:

How are the positions numbered?

All nucleotide and protein positions shown are based on reference sequence Yambuku-Mayinga (accession NC_002549).

How can I see the actual protein or nucleotide sequence of the feature?

To view the sequence, zoom in or click. The data you see when you click on features will include options to copy or download the sequence.

Can I download track data?

When you right-click (Ctrl-click) on any track, you will have the option to download the data in GFF, BED, or Sequin Table formats (see screenshot below). If you want more user-friendly formats, most of the data are also available from other locations on our website (see next question).

What are your data sources?

There is something I don't understand.

Please contact us. We will help you find what you need, and your comments will help us improve this tool.

 

Ebola gene names and CDS features
Short name CDS features Start* End* Frame
NP nucleoprotein 470 2689 2
VP35 polymerase complex protein 3129 4151 3
VP40 matrix protein 4479 5459 3
sGP small secreted glycoprotein 6039 7133 3
GP (part 1) spike glycoprotein (part 1) 6039 6923 3
GP (part 2) spike glycoprotein (part 2) 6923 8068 2
ssGP (part 1) second secreted glycoprotein (part 1) 6039 6922 3
ssGP (part 2) second secreted glycoprotein (part 2) 6924 6933 1
VP30 minor nucleoprotein 8509 9375 1
VP24 membrane-associated protein 10345 11100 1
L RNA-dependent RNA polymerase 11581 18219 1

*EBOV Mayinga strain coordinates (NC_002549)

 

Getting started: JBrowse features

You can also learn basic features from the screencast video at JBrowse.

These screenshots are based on the HIV Genome Browser, but the basic functions are the same for the Ebola browser.

Terminology: tracks and features

Mouseovers provide quick information, in brief.

helpfile image

View and put away tracks

helpfile image

Where am I?

Three places indicate your position (in Yambuku-Mayinga nucleotide or protein coordinates).

You can type a new coordinate into the box and go there.

helpfile image

Navigation: move right/left

There are 3 ways to move left and right:

  • Move the red position box.
  • Use the right/left arrow buttons.
  • Simply grab the workspace (click and hold) and move it.
helpfile image

Navigation: zoom

There are 3 ways to zoom:

  • Grab a section of the bar.
  • Use +/- buttons.
  • Type in the coordinates you want.
helpfile image

Get more information: click

Clicking on any feature will bring up additional localization information and sequence information.

helpfile image

Switch from nucleotide to protein view: right-click

From any nucleotide feature (except LTR features): right-click → Switch to protein view. This will open a new window with a browser for the relevant protein.

From the protein view, right-click → Switch to nucleotide view.

If your mouse doesn't have right-click, use Ctrl-click.

helpfile image

Move from one protein to another

From any protein view, you can switch to other proteins.

helpfile image

Track options

Click on down arrow for track options.

"Pin to top" will stick the track to the top of the screen and allows you to scroll down while still seeing that track (similar to "Freeze top row" in Excel.)

"Save track data" will provide download options.

helpfile image

Text Search

Type the name of any feature into the text box. If the name is recognized, a dropdown menu will offer options. Select the feature of interest and click 'Go'.

helpfile image

Highlight

Use right-click options to highlight any feature.

Highlighting can help you better visualize the co-location of features in different tracks.

If your mouse doesn't have right-click, use Ctrl-click.

helpfile image  

Remove highlight

Use View menu to clear highlight.

helpfile image  

 

Return to Ebola Genome Browser entry page.

 




Questions or comments? Contact us at hfv-info@lanl.gov