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Genome Browser

Introduction

The Genome Browser facilitates the visualization of various file types through a side-scrolling interface, where features are organized and displayed in sequence from left to right based on their start positions. Each file is depicted as a track within the browser, with support for multiple tracks including GFF, VCF, DNA Fasta, and BAM formats. Users have the flexibility to reorder, hide, or close tracks utilizing the provided track controls (). The visualization process allows for one chromosome to be viewed at any given time; this includes a comprehensive representation of the entire chromosome in the top box and a detailed view of the specific region currently under examination in the smaller box.

Figure 1:Genome Browser with all 4 tracks.

GFF Track

The GFF track is able to detect types to group features by genes (genes, transcripts, exons and CDS and the relationship between them by using ID and Parent attributes, see GFF3 Specification for more details ). Genes are in blue, the transcripts are the small red lines, non-coding exons are white boxes with orange border and exons with CDS are filled with orange color. Other non-grouped features appear in grey. GFF Viewer can be opened with the context menu option in the File Manager when selecting a GFF file and using the context menu option Show in GFF Viewer from the tablewhen exploring a GFF file.

With the Features button controls you can classify the types for Genes, Transcripts, Exons and CDS, this will modify the Gene group visualization, by default these types will be set automatically. The checkboxes will hide or show the features, i.e. if you want to show only the genes, you need to uncheck the Transcripts, Exon, CDS, and Unclassified checkboxes.

A tooltip will appear on mouse hover, it will show additional information about the feature and the information is collected from the GFF file.

Figure 2: GFF viewer.

Figure 3: Feature controls.

Figure 4. Feature tooltip.

VCF Track

The VCF track shows the variants in the corresponding position and if you zoom in enough, the alternative nucleotide will be shown.

Figure 5:VCF track

BAM Track

The BAM track shows the reads of a BAM file and if the sequence track is active, will also paint the differences between the read sequence and the sequence track. If you click on the checkbox, if the BAM has paired reads, the pair will be painted one beside the other.

Figure 6:BAM track

DNA Fasta Track

The DNA Fasta or sequence track shows the nucleotides and is only shown on low region lengths.

Figure 7:DNA Fasta Track

Navigation is executed using the mouse. To initiate scrolling, left-click and hold the button, then move the mouse horizontally to navigate left or right. Additionally, it is possible to focus on a specific feature or gene by double-clicking on it. Zooming in and out within the current region can be achieved through the "Zoom buttons" located on the Toolbar. Should you zoom out sufficiently, the display will transition to show a histogram for broader visualization purposes. The chromosome box allows for selection of new regions either by clicking directly or selecting a new box area through click-and-drag actions.

Figure 8. Histogram, the small rectangle on the Chromosome box shows the region painted as a histogram.

It is also possible to find features on the GFF and the VCF track using the Search field in the Toolbar, the search results will be shown on a panel beside the Toolbar.

Figure 9: Toolbar

Also, you can add more tracks to the current Genome Browser using the Add track button. A window will appear the available files that can be opened with a Genome Browser as tracks.

Figure 10:Browse tracks to be added to the Genome Browser

Load files

Files must be loaded in order to be shown on the Genome Browser to do that just click on the File menu and under the Load sub-menu you can load GFF, VCF, DNA Fasta and BAM files. These files can be loaded in either with .gff or .gz extension.

A window will appear to select the file to import, use the browse button to select the file from the file system and finally click on the Load button to start the Load process, the load time depends on the file size.

Genome Browser can also be opened from a Table view, If you have already a file open in a table, use the context menu option Show in Genome Browser, by right-clicking on a row, a Genome Browser will be shown on the region of that feature.

Once loaded you may save the file, once the file is saved you can visualize it using the Genome Browser.

Figure 11: Load Files to see in the browser

Figure 12:Browse for GFF file

Figure 13:Open the saved file directly with the Genome Browser

Figure 14: Open the Genome Browser from GFF table

Additional Resources