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HIV Genome Browser Help

What is the HIV Genome Browser?

This tool is a customization of JBrowse, built to incorporate many sources of information from the LANL HIV Sequence and Immunology databases.

Nucleotide views can include:

Protein views can include:

How are the positions numbered?

All nucleotide and protein positions shown are based on reference sequence HXB2 (or Mac239). Click information includes both nucleotide and protein coordinates.

What is entropy?

Entropy is a measure of the variability of each amino acid residue in an alignment. A position with a high entropy score is highly variable, while a position with low entropy is highly conserved. Values shown were calculated with our Entropy tool, based on our 2012 protein web alignments. We provide entropy values for M group (all subtypes of HIV-1) and for the two most prevalent subtypes, B and C. The entropy values for HIV-1 range from ~0.01 (highly conserved) to ~2.7 (hypervariable).

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 the track data?

When you right-click (Ctrl-click) on any track, you have the option to download the data in GFF, BED, or Sequin Table formats (see screenshot below). If you want other formats, some of the data are also available from other locations in our databases:

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.

 

Getting started: JBrowse features

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

Terminology: tracks and features

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View and put away tracks

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Where am I?

Three places indicate your position (in HXB2 nucleotide or protein coordinates).

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

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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.
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Navigation: zoom

There are 3 ways to zoom:

  • Grab a section of the bar.
  • Use +/- buttons.
  • Type in the coordinates you want.
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Get more information: click

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

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Switch from HXB2 to Mac239

From nucleotide view, you can switch between HXB2 and Mac239.

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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.

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Move from one protein to another

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

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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.

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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'.

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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.

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Remove highlight

Use View menu to clear highlight.

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last modified: Wed Feb 26 10:16 2014


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

 
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