Annals of Combinatorics 4 (2000) 247-255


Avoided Strings in Bacterial Complete Genomes and a Related Combinatorial Problem

Bailin Hao, Huimin Xie, Zuguo Yu, and Guoyi Chen

Institute of Theoretical Physics, Academia Sinica, P. O. Box 2735, Beijing 100080, China
hao@itp.ac.cn

Received December 12, 1998

AMS Subject Classification: 05A15, 92C40

Abstract. The visualization of avoided and under-represented strings in some bacterial complete genomes raises a combinatorial problem which may be solved either by using the Goulden-Jackson cluster method or by construction of the minimal finite automaton defined by the set of forbidden words of the corresponding language.

Keywords: complete genomes, avoided strings, language, enumeration, fractal


References

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4.  B.-L. Hao, H.-C. Lee, and S.-Y. Zhang, Fractals related to long DNA sequences and complete genomes, Chaos, Solitons and Fractals, 11 (2000) 825–836.

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6.  J. Noonan and D. Zeilberger, The Goulden–Jackson cluster method: extensions, applications and implementations; http://www.math.temple.edu/ ˜zeilberg.

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9.  Huimin Xie, Grammatical Complexity and One-Dimensional Dynamical Systems, World Scientific, Singapore, 1996.


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