mreps: efficient and flexible detection of tandem repeats in DNA

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 so...

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Bibliographic Details
Published in:Nucleic acids research 2003-07, Vol.31 (13), p.3672-3678
Main Authors: Kolpakov, Roman, Bana, Ghizlane, Kucherov, Gregory
Format: Article
Language:English
Subjects:
Algorithms
Computer Science
DNA - chemistry
DNA, Bacterial - chemistry
Genes, Bacterial
Genome, Human
Genomics - methods
Humans
Internet
Neisseria meningitidis - genetics
Other
Polymorphism, Genetic
Saccharomyces cerevisiae - genetics
Sequence Analysis, DNA - methods
Software
Tandem Repeat Sequences
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Summary: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/.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkg617