Fractals from genomes: exact solutions of a biology-inspired problem

Preprint

26 October 1999

preprint
Published by arXiv in arXiv

https://doi.org/10.48550/arXiv.cond-mat/9910422

Abstract

This is a review of a set of recent papers with some new data 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 constotuent strings. The calculation of their exact dimensions and the counting of true 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.

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All Related Versions

Version 1, 1999-10-26, ArXiv
Published version: Physica A: Statistical Mechanics and its Applications, 282 (1-2), 225.

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