A Fast Look-Up Algorithm for Detecting Repetitive DNA Sequences

Abstract

this paper, we focus on repetitive sequences in which short words are repeated many times, referred to as tandem repeats or microsatellites in the literature. We describe a linear time algorithm that can scan DNA sequences rapidly for tandem repeats. Recently, a new look-up technique, which uses indices calculated from non-contiguous, overlapping tuples, was employed in the FLASH program (Califano and Rigoutsos) for sequence homology search and is used here to recognize tandem repeats