mreps: efficient and flexible detection of tandem repeats in DNA
Abstract
The presence of repeated sequences is a fundamental feature of genomes. Tandemly repeated DNA appears in both eukaryotic and prokaryotic genomes, it is associated with various regulatory mechanisms, and plays an important role in genomic fingerprinting. In this paper, we describe {\mreps} -- a powerful software tool for a fast identification of tandemly repeated structures in DNA sequences. {\mreps} is capable to identify all types of tandem repeats within a single program run; it has a resolution parameter that allows the program to identify ``fuzzy'' repeats. We introduce main algorithmic solutions behind {\mreps}, describe its usage, give some execution time benchmarks, and present several case studies to illustrate its capabilities. The {\mreps} web interface is accessible through {\tt http://www.loria.fr/mreps/}.