LOCATION OF REPETITIVE REGIONS IN SEQUENCES BY OPTIMIZING A COMPRESSION METHOD
Olivier Delgrange, Max Dauchet, Éric Rivals · 1998
Suppose that a biologist wishes to study some local property P of genetic sequences. If he can design (with a computer scientist) an algorithm C which efficiently compresses parts of the sequence which satisfy P, then our algorithm TurboOptLift locates very quickly where property P occurs by chance on a sequence, and where it occurs as a result of a significant process. Under some conditions, the time complexity of TurboOptLift is O(n log n). We illustrate its use on the practical problem of locating approximate tandem repeats in DNA sequences.