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Nucleic Acids Research, Vol 25, Issue 16 3248-3254, Copyright © 1997 by Oxford University Press

ARTICLES

Enhancement of the nucleosomal pattern in sequences of lower complexity

A Bolshoy, K Shapiro, EN Trifonov and I Ioshikhes
Center for Biological Sequence Analysis, Department of Chemistry, The Technical University of Denmark, DK-2800 Lyngby, Denmark. alex@cbs.dtu.dk

Intuitively, the complexity of a given DNA sequence is related to the number of various superimposed biological messages it contains. Here we assess the expectation that in nucleosome DNA sequences of lower linguistic complexity, the nucleosome DNA positioning pattern would be more pronounced than in those of higher linguistic complexity. The nucleosome DNA positioning pattern is one of the weakest (highly degenerate) sequence patterns. It has been extracted recently by specially designed multiple alignment procedures. We applied the most sensitive of these procedures to nearly equal subsets of a nucleosome database separated according to linguistic complexity. The pattern extracted from the subset of the simpler nucleosome sequences not only possesses all major attributes of the known nucleosomal pattern, but is substantially stronger with respect to amplitude in comparison with the total database. This result constitutes the first demonstration that a weak pattern can be significantly enhanced by selective treatment of a lower complexity subset of the sequence ensemble under consideration.
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