GFF Viewer

The GFF viewer allows you visualize GFF files in a side-scrolling way. One sequence is visualized at a time, the top box represents the whole sequence, it also provides a feature density visualization represented with a gray to green gradient,  being gray low density and green high density, white is used when no features are on that region. Features are painted below ordered by start from left to right. Also GFF 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 table when exploring a GFF file.

Figure 1. Sample region area on SeqId 22, Start 19,938,770 and End 19,972,812.

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

Figure 2. Feature tooltip

Navigation is performed with the mouse, by left-clicking without releasing the button the scroll action will start, the just move the mouse to move left or right. Also is possible to adjust region to a feature or gene by double clicking on it, on the figure 2 we can see that the area is adjusted to see the COMT gene. Zoom in and Zoom out from current region is performed using the Zoom buttons on the Side Toolbar, If you zoom out enough, visualization will change and an histogram will show (see Figure 3).

Figure 3. Histogram, the small rectangle on the Seqid box shows the region painted as histogram.

The toolbar allows to modify the region by clicking on the Zoom buttons or writing a new region in the Navigation field. Non grouped features can be hide by using the Show genes only checkbox. Labels and tooltips can be enabled or disabled with the corresponding checkboxes. With the Gene drawing controls you can assign the types for Genes, Transcripts, Exons and CDS, this will modify the Gene group visualization, by default this types will be set automatically.

Figure 4. GFF viewer Toolbar controls.