Pseudomonas Genome Database - Overview

How to Display and Configure Different GBrowse Tracks

Pseudomonas GBrowse (based on software developed by Stein et al., 2002) provides an alternate presentation of all the bacterial genomes in the database. By selecting boxes on the GBrowse start page, the user can select a specific strain and annotation information to view including alternate gene names, protein names, motifs/structures as well as metabolic pathway data and knockout data, and perform a search based on criteria they specify. GBrowse then fetches the region of genome specified by the user's search criteria and presents the specified landmarks to the user in a detailed view containing one or more horizontal tracks representing individual sequence features for that area (Fig. 6a). The user is free to zoom in and out according to the level of magnification/resolution desired (Fig. 5: blue arrow). Landmarks on each track usually contain a link to detailed information on additional web sites.

Selecting Features to View

The GBrowse Select Tracks tab lists all available tracks that can be viewed. In order to select or remove a track, click on the Select Tracks tab and select/deselect checks from the boxes (Fig. 6b). If you wish to view tracks of annotations for another genome in the database, simply go back to the main Browser tab and select the organism/genome name from the drop down box above the tracks (Fig. 6a: black arrow).

Finding a Region

You can quickly jump to another specific region of the genome by entering the coordinates in the Landmark or Region box (Figure 6a: orange arrow) or by highlighting the region in the Overview, Region or Details panels. (Fig. 6a: blue arrows).

Ordering Tracks

One can also specify the order by which a track appears by dragging the title bar (Fig 6a: red arrows) to another position on the screen.

Finding a description for a specific track's data

Each track's title bar also contains a link (?) to a text box giving more details about the track, including source of the data and an overview of the methods used. The list of tracks in the "Select Tracks" table will contain a similar link to this documentation.

Downloading track data

If you would like to download data from any of the tracks, select 'Download Track Data' from the drop-down list to the right side above the tracks and any data associated with the current view will be downloaded in GFF3 format. More advanced options, including setting the download to include features across the entire genome or embed the sequence into the download file, can be set by clicking on 'Configure' to the right of the list.

Sharing views

If you wish to share the current screenshot with others, or export an image of it, simply go the 'File' link at the top left of the page where you can select 'Bookmark this' to get a permanent link or select 'Export as...' for a list of suggested ways to export your image.

Figure 6a: Main GBrowse panel for viewing and navigating annotations in a genome.

Figure 6b: GBrowse panel for configuring display of annotation tracks.

How to Upload Your Own Data to GBrowse

It is also possible to upload your own data to GBrowse to view it in the context of other genome annotations. To do this you would first have to convert it into GFF format. Important: The first column must contain the RefSeq accession for the chromosome or plasmid you wish to associate with your uploaded data. For P. aeruginosa PAO1, this would be NC_002516. If you are unsure of what the RefSeq accession is, go to the Browser tab and view the RefSeq accession in the Landmark or Region box OR check the URL window of your browser for the value following "ref=".

For additional information on getting your data to follow this format, you can download track data by selecting from the drop-down box (Fig 6c: red arrow) and clicking on Go.

Figure 6c: How to download track data from GBrowse.

Once you have your data in GFF format, select the Custom Tracks tab (Fig. 6c: orange arrow) which will bring you to a web form with options to paste data or link to/upload a GFF file. You can choose from 3 options:

1): Copy and paste your data into a web form - Click on the "[From text]" link and paste your data into the web form that appears underneath (Figure 6e). This is suitable if you have a small number of features to view.

Figure 6d: Using the upload form under "Custom Tracks"

Figure 6e: View of the web form for pasting GFF-formatted data.

2): Upload a GFF file containing your data - Click on the "[From a file]" link, choose your file and click on the upload button (Figure 6d). This is the most common choice for users, especially when you have a large amount of data.

3): Provide a URL to a GFF file on another server - Click on the "[From a URL]" link (Figure 6d), choose your file and click on the Import button.

Troubleshooting

If your track of data does not appear right away, go to the Select Tracks tab and make sure the box associated with your custom track is checked.

If the track label is present but no data is appearing, make sure you are using the correct RefSeq accession in column 1 of your data.

More details on uploading data to GBrowse can be found in the GBrowse documentation.

How to Upload and View RNA-Seq Data in GBrowse

GBrowse is capable of displaying XY plots, density plots and individual reads based on the standard SAM/BAM file format output by most alignment tools. In order to upload your own BAM alignment files into GBrowse, go to 'Custom Tracks' and click on 'From a file' and select a sorted BAM file stored on your computer. The most important considerations when uploading this kind of data are

  • The recommended maximum file size is 200 MB. While many bam files are much larger than this, we recommend filtering the number of raw reads in a step prior to sorting the bam file, which should still provide an adequate representation for visualization purposes. If a server error is encountered after upload, try reducing the size of the bam file being uploaded by following the suggestions above. If an individual RNA-Seq displays a time-out error while loading, consider zooming in on a smaller area.
  • Ensure that the sequence name reads are mapped to is matching the GBrowse RefSeq accession found in the 'Landmark or Region' box (e.g. NC_002516 for P. aeruginosa PAO1). Provided they are the same, the uploaded BAM file will be automatically indexed when the upload completes.

If the file is successfully uploaded, a coloured box containing the file name, date and number of bytes will appear under 'Source files'. The track should appear by default and have a name matching the name of the uploaded file. You can also edit an automatically generated configuration file in order to specify how your track appears by clicking on the '[edit]' link while further help with customizing the basic appearance such as height and colour of the figure is provided on a help page linked to from the top of 'Custom Tracks' box.

If you wish to share the current screenshot with others, or export an image of it, simply go the 'File' link at the top left of the page where you can select 'Bookmark this' to get a permanent link or select 'Export as...' for a list of suggested ways to export your image.