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

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

1999-10-26

arxiv.org/abs/cond-mat/9910422v1

Physics

Condensed Matter

Soft Condensed Matter

24 pages, LaTeX, 5 PostScript figures (two in color), psfig

Scientific paper

10.1016/S0378-4371(00)00102-3

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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