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mreps: efficient and flexible detection of tandem repeats in DNA

Identifieur interne : 001D01 ( Istex/Corpus ); précédent : 001D00; suivant : 001D02

mreps: efficient and flexible detection of tandem repeats in DNA

Auteurs : Roman Kolpakov ; Ghizlane Bana ; Gregory Kucherov

Source :

Nucleic Acids Research [ 0305-1048 ] ; 2003-07-01.

RBID : ISTEX:7C83591DA4DCBA20FC7287D8834B96E60103F431

English descriptors

Teeft :
- Algorithm, Approximate tandem, Case studies, Certain artifacts, Chromosome, Combinatorial, Combinatorial algorithm, Complete genome sequence, Computer science, Copy number, Corresponding tandem, Different resolution values, Error rate, Exhaustive manner, Exponent, Fundamental feature, Gcac acac, Genome, Genomic, Genomic sequence, Genomic sequences, Heuristic, Heuristic treatment, Human chromosome, Human disease, Lecture notes, Lower frame, Lter, Maximal, Maximal number, Mismatch, Mismatch errors, Mreps, Mreps output, Nding, Nding tandem, Neisseria, Neisseria meningitidis, Nucleic, Nucleic acids, Nucleic acids research, Occulation genes, Other hand, Pattern size, Random sequence, Recombination, Remarkable feature, Resolution level, Resolution parameter, Resolution values, Roman kolpakov, Same period, Short tandem, Software, Substitution errors, Tandem, Tandem arrays, Tandemly, Threshold error rate, True period, Whole genome, Whole genomic sequence.

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/.

Url:

https://api.istex.fr/ark:/67375/HXZ-MNH2TT43-R/fulltext.pdf

DOI: 10.1093/nar/gkg617

Links to Exploration step

ISTEX:7C83591DA4DCBA20FC7287D8834B96E60103F431

Le document en format XML

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<aff>French–Russian Institute for Informatics and Applied Mathematics, Moscow University, 119899 Moscow, Russia</aff>
<aff id="GKG617A1"><label>1</label>
INRIA-Lorraine/LORIA, 615, rue du Jardin Botanique, BP 101, 54602 Villers-lès-Nancy, France</aff>
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<author-notes><corresp id="COR1">*To whom correspondence should be addressed. Tel: +33 3 83 59 30 21; Fax: +33 3 83 27 83 19; Email: <ext-link xlink:href="gregory.kucherov@loria.fr" ext-link-type="email">gregory.kucherov@loria.fr</ext-link>
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<pub-date pub-type="ppub"><day>01</day>
<month>07</month>
<year>2003</year>
</pub-date>
<volume>31</volume>
<issue>13</issue>
<fpage>3672</fpage>
<lpage>3678</lpage>
<permissions><copyright-year>2003</copyright-year>
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<abstract xml:lang="en">

      <p>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 <monospace>mreps</monospace>
, a powerful software tool for a fast identification of tandemly repeated structures in DNA sequences. <monospace>mreps</monospace>
 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 <monospace>mreps</monospace>
, describe its usage, give some execution time benchmarks and present several case studies to illustrate its capabilities. The <monospace>mreps</monospace>
 web interface is accessible through <ext-link xlink:href="http://www.loria.fr/mreps/" ext-link-type="url">http://www.loria.fr/mreps/</ext-link>
.</p>

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<notes><p content-type="arthw-misc">Received February 15, 2003; Revised and Accepted April 2, 2003</p>
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