Speeding up the detection of evolutive tandem repeats

Abstract

We recently introduced evolutive tandem repeats with jump (using Hamming distance) (Proc. MFCS’02: the 27th Internat. Symp. Mathematical Foundations of Computer Science, Warszawa, Otwock, Poland, August 2002, Lecture Notes in Computer Science, Vol. 2420, Springer, Berlin, pp. 292–304) which consist in a series of almost contiguous copies having the following property: the Hamming distance between two consecutive copies is always smaller than a given parameter e. In this article, we present a significative improvement that speeds up the detection of evolutive tandem repeats. It is based on the progressive computation of distances between candidate copies participating to the evolutive tandem repeat. It leads to a new algorithm, still quadratic in the worst case, but much more efficient on average, authorizing larger sequences to be processed.