Genome Browser


Accessing the Genome Browser on the PATRIC Website

Each Organism on PATRIC has an Organism Landing Page. To get to this page at the Genus level, select your Genera of interest from the Organisms tab on the PATRIC homepage. The phylogeny of each Landing Page is listed across the top of the page. Once on the Genera Landing Page, you may access the Genome Browser by drilling down in one of the following ways to either the Genome or the Feature level:

  • Select the Genome List tab and click on your Genome Name of interest. This will take you to the chosen Genome-level Landing Page. At all Genome and Feature-level Landing Pages, the Genome List tab at the top of the page changes to a Genome Browser tab providing direct access to the Tool.
  • Select the Genome List tab and click on any Genome Browser  icon within the table to visually explore a specific genome.
  • Select the Feature Table tab and click on any Genome Browser  icon within the table.

You may also access the Genome Browser from within any PATRIC table you create while using PATRIC Searches and Tools where you see the Genome Browser icon.  To learn more about PATRIC Tables and how data is organized on PATRIC, see our Video Tutorials and Feature Table FAQs.

At Feature-level Landing Pages, you will also have a Compare Region Viewer tab.  For more information on the Compare Region Viewer, see below.


Genome Browser Overview

The Genome Browser is a graphical representation of the alignment of genes and other genomic data depicted along a central horizontal axis of genome coordinates.


Genome Browser Features and Functionality

Genome Browser Main Window:

  • Pan to a region of interest in the genome by:
    • Using the forward and backward arrow buttons at the top of the Browser.
    • Clicking and dragging the red slide bar located within the genome coordinate axis.
    • Entering your own start and/or end coordinates in the coordinate field and clicking on the “Go” button.
  • Zoom in/out to regions of interest by using the + and – buttons along the top of the Browser.  The larger buttons will zoom further in/out with one click than the smaller buttons.

Note: Once you reach a zoom level of approximately 1,300 base pairs or less a color-coded DNA sequence track (with associated AAs) will appear for the Reference Sequence.  Zooming in to 150 base pairs or less will label the NAs and AAs with the corresponding letter.

A = green, T = red , C = blue , G = yellow.

  • Any specific area you are viewing in the genome browser may be saved for the future via clicking the “Link” button in the upper right.  Copy this url and share it or save it and visit the same area at another time.
  • Using a yellow highlighter, you may highlight a region of the browser.  To do this either select the highlighter icon (in the zoom bar) and then click and drag an area of the browser window or use the View menu in the top left.  Clear highlighted sections via the View menu.

Note: A highlighted notation will remain when using the Link tool.

  • Use the Help menu in the top left corner of the browser to access general JBrowse Help or PATRIC’s Genome Browser FAQs.

Interacting with Browser Tracks and Downloading Track/Sequence Data:

  • The Genome Browser will initially open showing both PATRIC (blue) and RefSeq (green) annotated data tracks.  To learn more about various annotation sources, see Annotation FAQs.
  • Additional tracks, such as those annotated by Legacy BRCs, are located in the Available Tracks column, along the left side of the Genome Browser.
    • To add or remove tracks from the Genome Browser, simply click and drag them between the “Available Tracks” column and the browser window.
    • You may also remove tracks from the browser window by clicking on “Remove Track” from the drop-down menu next to the annotation source label or clicking on the “x” on the annotation source label.
  • From the drop down menu (accessed by hovering over the Reference sequence track label,) you may see information about the track, pin the track to the top row in the browser, edit the tracks configuration, remove the track to the Available Tracks column, save track data, and chose to show/hide forward strand, reverse strand, and translation.
    • When saving track data, you may chose to view or download either the “visible region” or the “whole reference genome” in FASTA format.
  • From the drop down menu (accessed by hovering over any Annotation track label,) you may see information about the track, pin the track to the top of the row in the browser, edit the tracks configuration, remove the track to the Available Tracks column, save the track data, or show/hide feature labels.
    • When saving track data, you may chose to view or download either the “visible region” or the “whole reference genome” in one of the three following formats:  GFF3, BED, or Sequin Table.

Uploading Your Own Tracks and Adding Custom Tracks:

  • Upload and view your own annotations or gene lists as GFF3 files and view them as tracks on the genome browser by selecting “Open” from the File menu in the top left corner of the browser.
  • Upload and view your RNA-Seq, ChIP-Seq, or SNP data as BigWig or BAM files and view them as tracks in the genome browser by selecting “Open” from the File menu in the top left corner of the browser.
  • You may also create tracks showing specific regions of the Reference Sequence (or it’s translations) by entering the NA or AA sequence.  To do this, select “Add sequence search track” from the file menu.

Interacting with Individual Browser Features and Accessing Feature Sequence Data:

  • Different genomic feature types annotated by the same source are grouped together as single tracks, using various shades of the same color to represent different feature types.  i.e. PATRIC annotations, shown in blue, will range from light blue to darker blue depending on the feature type.
  • Hovering over any feature within the Browser will display information such as Locus Tag, Location, Strand, Type, Gene Symbol, and Product.
  • Clicking on any feature within the Browser will open a pop-up with feature details and, if applicable, links to the Genome Browser, Compare Region Viewer, Associated Pathways, Transcriptomics Data, and Correlated Genes for that particular feature.  The pop-up also contains the NA sequence for the feature.

Compare Region Viewer

The Compare Region Viewer, implemented using JBrowse and data APIs provided by the SEED, allows researchers to compare genomic regions around a gene of interest across other closely related genomes. Using this viewer, one can quickly detect differences in translation start sites, potential frame shifts, or missing genes. This Viewer is interactive in the same manner as the Genome Browser with the addition of the following:

  • Coloring is based on protein functions and allows users to visually group proteins with similar functions.
  • You may change the size of the region and number of genomes compared in fields located above the coordinate axis.
  • Genomes displayed may be filtered and sorted based on key metadata attributes, such as isolation country, host, disease, collection date, and completion date.  Use the Select Tracks buttons in the top left to chose which genomes are shown/hidden and access metadata filtering.

This viewer can be accessed via the Compare Region Viewer tab available on feature-level pages.


Source

PATRIC offers Ajax-based genome browser implemented using JBrowse (Skinner et al, 2009).