DNA Rotator Walk

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The DNA rotator walk works by reading the DNA sequence one base at a time (, , , or ), turning through an angle that depends on the DNA base, and moving ahead by one step. For example, one might choose for (clockwise), for (counterclockwise), for (counterclockwise), and ° for (clockwise). The directions chosen for each base are indicated by the colored arrows at the top of the graphic. The starting point is indicated by a larger dot, and the starting direction is always upward. The DNA sequence used here is a 1000-bp region taken from a chicken gene called embryonic skeletal MHC. The gene region includes an exon surrounded by two introns. This visualization is useful to get an intuition for the properties of a DNA sequence. For example, with appropriate choices of angles, long repeat sequences such as poly- sequences ("") will produce localized circles, and sequences with equal mixtures of bases will tend to produce randomized regions.

Contributed by: Paul-Jean Letourneau (March 2011)
Open content licensed under CC BY-NC-SA


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