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

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-ov...

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Bibliographic Details
Published inPhysica A Vol. 282; no. 1; pp. 225 - 246
Main Author Hao, Bai-Lin
Format Journal Article
LanguageEnglish
Published Elsevier B.V 01.07.2000
Subjects
Bacteria
Bacteriology
DNA
DNA sequences
Formal languages
Fractal
Genes
Goulden–Jackson cluster method
Language theory
Numerical methods
Problem solving
Fractal
Language theory
87.14
DNA
87.23
Goulden–Jackson cluster method
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Summary: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 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.
Bibliography:ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-1
content type line 23
ISSN:0378-4371
1873-2119
DOI:10.1016/S0378-4371(00)00102-3