Fractals From Genomes - Exact Solutions of a Biology-Inspired Problem
B L Hao
Physica A , 282(1-2):225-246 (july 1, 2000)
Abstract
This is a review of a few recent papers with some new results added.
After a brief biological introduction a visualization scheme of the
string composition of long DNA sequences, in particular, of bacterial
complete genomes, will be described. This scheme leads to a class of
self-similar and self-overlapping fractals in the limit of infinitely long
constituent strings. The calculation of their exact dimensions and
the counting of hue and redundant avoided strings at different string
lengths turn out to be one and the same problem. We give exact solution
of the problem using two independent methods: the Goulden-Jackson
cluster method in combinatorics and the method of formal language theory.
