What is a Circle Graph?

A circle graph is one way to display base pairs of a structure. It also represents a first step to producing a formal structure in which overlap of bases is usually small.

Steps to make a circle graph:

1. Place the bases of a sequence equally around a circle in a clockwise fashion.
2. Indicate paired bases by drawing an arc between them. The arc is drawn as part of a circle that is perpendicular to the original circle at both bases.   Example.ps

Pseudoknots show up as intersecting arcs. Otherwise, the arcs do not intersect.

Steps to make a structure from a circle graph:

1. When dots are drawn on the middle of each arc to represent base pairs, the line connecting base pairs within a helix has a well defined angle. Example.ps Example.ps without arcs
   Within a structure, each angle can be drawn outward from a loop at this angle.
2. Bases which are not in a helix can be drawn around the loop between neighboring helices to form a structure. Example.ps structure
   In this way, a structure can be drawn.

If helices from a common loop in the circle graph are connected with lines, the intersection of the lines corresponds to a loop in the circle graph.
Example.ps without arcs and Example.ps

Summary:

The circle graph is useful for two reasons:

1. Indicating base pairs.
2. Providing the angles to draw helices in proper structures in which bases do not overlap (or where the overlap is at worst minimal).

Circle Graphs generated from this page correspond to structures drawn with Auto Rotate set to Off, and Format set to Default or simple, and no Rotation, and Exterior Loop set to Default.

Details

• G-C arcs are drawn in red.
• A-U, A-T arcs are drawn in blue.
• G-U, G-T arcs are drawn in green.
• Other arcs, if present, are in yellow.

Other options are to draw the arcs in all red, or to use p-num or ss-count values to find an average value for each base pair and color the arc accordingly.

The bases are drawn clockwise around the circle and lead to a structure in which bases are drawn clockwise around each loop.

This is a common way of producing a structure, but a counter-clockwise circle graph and resulting structure can be produced by placing the bases around the circle in a counter-clockwise fashion.