Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences.
BACKGROUND
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.
Rivals
E
E
Laboratoire d'Informatique Fondamentale de Lille, CNRS URA 369, Villeneuve d'Ascq, France. rivals@lifl.fr
Delgrange
O
O
Delahaye
J P
JP
Dauchet
M
M
Delorme
M O
MO
Hénaut
A
A
Ollivier
E
E
D000465:Algorithms; D001483:Base Sequence; D015825:Chromosomes, Fungal / Q000235:genetics; D004247:DNA / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics; D005069:Evaluation Studies as Topic; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods / Q000706:statistics & numerical data; D012984:Software
D004271:DNA, Fungal; D004247:DNA