Visualization of DNA Sequence Features Based on Cellular Automata

Huang, Qingnan; Wang, Xuanqi; Li, Huili; He, Feng; Wu, Xiaoming

Visualization of special patterns in biological sequences can assist revealing important roles in gene regulation and other basic molecular activities of the sequence. The visualization method needs to highlight interesting sequence patterns while suppressing trivial aspects. A biology sequences visualization scheme based on cellular automata is developed in this study. Features such as alleles of a DNA sequence were extracted and mapped into a grid in a two-dimensional plane, creating an initial pattern. Then, two-dimensional cellular automata were iteratively executed according to predefined rules and turned the initial pattern into a two-dimensional pattern, forming the fingerprint of the sequence. This fingerprint can be served as a representation of the sequence and can be used to make sequences comparing.