Show a Plot of GC Content

How do I display GC content (% G+C) next to a DNA sequence?

The option to show a "GC Content" plot is available in SnapGene 5.2 and later.

The SnapGene GC Content plot represents the %G+C ( {G or C} / {A or T or G or C} ) for a sliding window of length 25 nucleotides. Degenerate positions are counted as a fraction of G or C.

Open a DNA Sequence

Open a DNA sequence file, and display the sequence in Map view.

Turn on Display of "GC Content"

Click the "Choose color option" drop-down button in the side toolbar, and choose "GC Content".  The adjacent button icon will indicate that a GC content plot is displayed.

A plot of "% GC" will be shown above the DNA line.

Hovering the pointer in Map view will report "% GC" for that position on the graph. For larger sequences, the pixel under the pointer will represent more than one nucleotide position, so a range will be reported (in the above example positions 8299..8325). The reported "% GC" will represent the average "% GC" for all nucleotide positions in the range.

Configure the Plot

By default, the midpoint for the color range is set to the average %GC for the sequence. To adjust this midpoint, use the slider to the right of the plot.

Click on the range markers next to the slider to open a dialog for adjusting the total color range and the midpoint for the color range.

To see a plain graph, choose "No colors".

Click the axis label to the left of the plot to open a dialog for adjusting the minimum and maximum %GC values.

To export an image of the DNA map with the associated GC content plot, click File → Export Map.

Display Colored Bases in Sequence View

When the "GC Content" display option is chosen in Sequence view, G and C bases will be colored red while A and T bases will be colored blue.