title: 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 able to identify all types of tandem repeats within a single run on a whole genomic sequence. 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 http://www.loria.fr/mreps/.
authors.affiliation: French-Russian Institute for Informatics and Applied Mathematics, Moscow University, 119899 Moscow, Russia.
authors.forename: Roman
authors.initials: R
authors.lastname: Kolpakov
authors.forename: Ghizlane
authors.initials: G
authors.lastname: Bana
authors.forename: Gregory
authors.initials: G
authors.lastname: Kucherov
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry; D004269:DNA, Bacterial / Q000737:chemistry; D005798:Genes, Bacterial; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D020407:Internet; D009345:Neisseria meningitidis / Q000235:genetics; D011110:Polymorphism, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D020080:Tandem Repeat Sequences
chemical_list: D004269:DNA, Bacterial; D004247:DNA