Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences
1997
Rivals, E. | Delgrange, O. | Delahaye, J.P. | Dauchet, M. | Delorme, M.O. | Henaut, A. | Ollivier, E.
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.
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