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© Oxford University Press

Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences

E. Rivals 1,4, O. Delgrange 2, J.-P. Delahaye 1, M. Dauchet 1, M.-O. Delorme 3, A. Hénaut 3 and E. Ollivier 3

1Laboratoire d'Informatique Fondamentale de Lille CNRS URA 369, Villeneuve d'Ascq 59655, France
2Université de Mons-Hainaut Mons, B7000, Belgium
3Université de Versailles Saint-Quentin Versailles 78035, France

4To whom correspondence should be addressed

MOTIVATION: Compression algorithms can be used to analyse genetic sequences. A compression algorithm tests a given property on the sequence and uses it to encode the sequence: if the property is true, it reveals some structure of the sequence which can be described briefly, this yields a description of the sequence which is shorter than the sequence of nucleotides given in extenso. The more a sequence is compressed by the algorithm, the more significant is the property for that sequence.

RESULTS: We present a compression algorithm that tests the presence of a particular type of dosDNA (defined ordered sequence-DNA): approximate tandem repeats of small motifs (i.e. of lengths <4). This algorithm has been experimented with on four yeast chromosomes. The presence of approximate tandem repeats seems to be a uniform structural property of yeast chromosomes.

AVAILABILITY: The algorithms in C are available on the World Wide Web (URL: http://www.lifl.fr/~rivals/Doc/RTA/).

CONTACT: E-mail: rivals{at}lifl.fr

Received on March 27, 1996; revised on July 29, 1996; accepted on August 22, 1996

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