mreps: efficient and flexible detection of tandem repeats in DNA
Identifieur interne : 001949 ( Istex/Checkpoint ); précédent : 001948; suivant : 001950mreps: efficient and flexible detection of tandem repeats in DNA
Auteurs : Roman Kolpakov ; Ghizlane Bana [France] ; Gregory Kucherov [France]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2003-07-01.
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:
DOI: 10.1093/nar/gkg617
Affiliations:
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Acids Res.</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2003-07-01">2003-07-01</date><biblScope unit="volume">31</biblScope><biblScope unit="issue">13</biblScope><biblScope unit="page" from="3672">3672</biblScope><biblScope unit="page" to="3678">3678</biblScope></imprint><idno type="ISSN">0305-1048</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Algorithm</term><term>Approximate tandem</term><term>Case studies</term><term>Certain artifacts</term><term>Chromosome</term><term>Combinatorial</term><term>Combinatorial algorithm</term><term>Complete genome sequence</term><term>Computer science</term><term>Copy number</term><term>Corresponding tandem</term><term>Different resolution values</term><term>Error rate</term><term>Exhaustive manner</term><term>Exponent</term><term>Fundamental feature</term><term>Gcac acac</term><term>Genome</term><term>Genomic</term><term>Genomic sequence</term><term>Genomic sequences</term><term>Heuristic</term><term>Heuristic treatment</term><term>Human chromosome</term><term>Human disease</term><term>Lecture notes</term><term>Lower frame</term><term>Lter</term><term>Maximal</term><term>Maximal number</term><term>Mismatch</term><term>Mismatch errors</term><term>Mreps</term><term>Mreps output</term><term>Nding</term><term>Nding tandem</term><term>Neisseria</term><term>Neisseria meningitidis</term><term>Nucleic</term><term>Nucleic acids</term><term>Nucleic acids research</term><term>Occulation genes</term><term>Other hand</term><term>Pattern size</term><term>Random sequence</term><term>Recombination</term><term>Remarkable feature</term><term>Resolution level</term><term>Resolution parameter</term><term>Resolution values</term><term>Roman kolpakov</term><term>Same period</term><term>Short tandem</term><term>Software</term><term>Substitution errors</term><term>Tandem</term><term>Tandem arrays</term><term>Tandemly</term><term>Threshold error rate</term><term>True period</term><term>Whole genome</term><term>Whole genomic sequence</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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/.</div></front></TEI><affiliations><list><country><li>France</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Villers-lès-Nancy</li></settlement></list><tree><noCountry><name sortKey="Kolpakov, Roman" sort="Kolpakov, Roman" uniqKey="Kolpakov R" first="Roman" last="Kolpakov">Roman Kolpakov</name></noCountry><country name="France"><region name="Grand Est"><name sortKey="Bana, Ghizlane" sort="Bana, Ghizlane" uniqKey="Bana G" first="Ghizlane" last="Bana">Ghizlane Bana</name></region><name sortKey="Kucherov, Gregory" sort="Kucherov, Gregory" uniqKey="Kucherov G" first="Gregory" last="Kucherov">Gregory Kucherov</name><name sortKey="Kucherov, Gregory" sort="Kucherov, Gregory" uniqKey="Kucherov G" first="Gregory" last="Kucherov">Gregory Kucherov</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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