GC Content track

To display the GC Content track:

GC Content is a graph track with a scale from 0-100 showing the proportional amount of G or C residues in a sliding window of user-defined width.

The visibility of GC Content tracks in the Sequences view is available only for nucleotide (DNA) sequences, and is dependent on:

• Whether or not tracks are visible in the Sequences view. To display tracks, click on the plus sign next to the sequence of interest.

• Whether or not the GC Content box is checked in the Tracks panel. This box is only visible for nucleotide sequences.

To change GC Content options:

To learn how to access the options section for this track, see Tracks.

• Calculations are performed in a sliding window. Type a number in the Window size box to specify the number of consecutive residues to use in the GC content calculation. The window size may be any integer from 1-5,000, and the default is 25 residues. The window shifts along sequences one position at a time, and will therefore overlap for widths greater than 1.

*Note: the GC value at each residue is computed using a window centered over the residue in the ungapped sequence. An even window width causes the window to be slightly off-center. As the window approaches either end of the sequence, one side will stop moving, and the window will shrink.

• By default, GC Content is shown in tones of blue. To choose another color, click on the color box to the right of Line color.

Click if you wish to return to the default values.