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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><monospace>mreps</monospace>: efficient and flexible detection of tandem repeats in DNA</title><author><name sortKey="Kolpakov, Roman" sort="Kolpakov, Roman" uniqKey="Kolpakov R" first="Roman" last="Kolpakov">Roman Kolpakov</name></author><author><name sortKey="Bana, Ghizlane" sort="Bana, Ghizlane" uniqKey="Bana G" first="Ghizlane" last="Bana">Ghizlane Bana</name><affiliation><nlm:aff id="N0x9857888.0x98ae3c0"></nlm:aff></affiliation></author><author><name sortKey="Kucherov, Gregory" sort="Kucherov, Gregory" uniqKey="Kucherov G" first="Gregory" last="Kucherov">Gregory Kucherov</name><affiliation><nlm:aff id="N0x9857888.0x98ae3c0"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">12824391</idno><idno type="pmc">169196</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169196</idno><idno type="RBID">PMC:169196</idno><date when="2003">2003</date><idno type="wicri:Area/Pmc/Corpus">000021</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000021</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><monospace>mreps</monospace>: efficient and flexible detection of tandem repeats in DNA</title><author><name sortKey="Kolpakov, Roman" sort="Kolpakov, Roman" uniqKey="Kolpakov R" first="Roman" last="Kolpakov">Roman Kolpakov</name></author><author><name sortKey="Bana, Ghizlane" sort="Bana, Ghizlane" uniqKey="Bana G" first="Ghizlane" last="Bana">Ghizlane Bana</name><affiliation><nlm:aff id="N0x9857888.0x98ae3c0"></nlm:aff></affiliation></author><author><name sortKey="Kucherov, Gregory" sort="Kucherov, Gregory" uniqKey="Kucherov G" first="Gregory" last="Kucherov">Gregory Kucherov</name><affiliation><nlm:aff id="N0x9857888.0x98ae3c0"></nlm:aff></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="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 ext-link-type="uri" xlink:href="http://www.loria.fr/mreps/">http://www.loria.fr/mreps/</ext-link>.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-title>Nucleic Acids Research</journal-title><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name><publisher-loc>Oxford, UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">12824391</article-id><article-id pub-id-type="pmc">169196</article-id><article-id pub-id-type="publisher-id">gkg617</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title><monospace>mreps</monospace>: efficient and flexible detection of tandem repeats in DNA</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kolpakov</surname><given-names>Roman</given-names></name></contrib><contrib contrib-type="author"><name><surname>Bana</surname><given-names>Ghizlane</given-names></name><xref ref-type="aff" rid="N0x9857888.0x98ae3c0">1</xref></contrib><contrib contrib-type="author"><name><surname>Kucherov</surname><given-names>Gregory</given-names></name><xref ref-type="aff" rid="N0x9857888.0x98ae3c0">1</xref><xref ref-type="author-notes" rid="gkg617fn1">*</xref></contrib></contrib-group><aff id="N0x9857888.0x98ae3c0">French–Russian Institute for Informatics and Applied Mathematics, Moscow University, 119899 Moscow, Russia<label>1</label>INRIA-Lorraine/LORIA, 615, rue du Jardin Botanique, BP 101, 54602 Villers-lès-Nancy, France</aff><author-notes><fn id="gkg617fn1"><label>*</label><p>To whom correspondence should be addressed. Tel: +33 3 83 59 30 21; Fax: +33 3 83 27 83 19; Email: <email>gregory.kucherov@loria.fr</email></p></fn></author-notes><pub-date pub-type="ppub"><day>1</day><month>7</month><year>2003</year></pub-date><volume>31</volume><issue>13</issue><fpage>3672</fpage><lpage>3678</lpage><ext-link ext-link-type="uri" xlink:href="http://www.nar.oupjournals.org/content/vol31/issue13//"></ext-link><history><date date-type="received"><day>15</day><month>2</month><year>2003</year></date><date date-type="rev-recd"><day>2</day><month>4</month><year>2003</year></date><date date-type="accepted"><day>2</day><month>4</month><year>2003</year></date></history><copyright-statement>Copyright © 2003 Oxford University Press</copyright-statement><copyright-year>2003</copyright-year><abstract><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 ext-link-type="uri" xlink:href="http://www.loria.fr/mreps/">http://www.loria.fr/mreps/</ext-link>.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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