KMC 3: counting and manipulating k-mer statistics.
Identifieur interne : 000C96 ( PubMed/Curation ); précédent : 000C95; suivant : 000C97KMC 3: counting and manipulating k-mer statistics.
Auteurs : Marek Kokot [Pologne] ; Maciej Dlugosz [Pologne] ; Sebastian Deorowicz [Pologne]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- methods : Computational Biology.
- Algorithms, Animals, Chickens, Databases, Factual, Humans, Software.
Abstract
Counting all k -mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k -mer databases. Usefulness of the tools is shown on a few real problems.
DOI: 10.1093/bioinformatics/btx304
PubMed: 28472236
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Gliwice 44-100, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice 44-100</wicri:regionArea></affiliation></author><author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice 44-100, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice 44-100</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno 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Electronics and Computer Science, Silesian University of Technology, Gliwice 44-100</wicri:regionArea></affiliation></author><author><name sortKey="Dlugosz, Maciej" sort="Dlugosz, Maciej" uniqKey="Dlugosz M" first="Maciej" last="Dlugosz">Maciej Dlugosz</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice 44-100, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice 44-100</wicri:regionArea></affiliation></author><author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice 44-100, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice 44-100</wicri:regionArea></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Chickens</term><term>Computational Biology (methods)</term><term>Databases, Factual</term><term>Humans</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Bases de données factuelles</term><term>Biologie informatique ()</term><term>Humains</term><term>Logiciel</term><term>Poulets</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Chickens</term><term>Databases, Factual</term><term>Humans</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Bases de données factuelles</term><term>Biologie informatique</term><term>Humains</term><term>Logiciel</term><term>Poulets</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Counting all k -mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k -mer databases. Usefulness of the tools is shown on a few real problems.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">28472236</PMID><DateCompleted><Year>2018</Year><Month>03</Month><Day>26</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>33</Volume><Issue>17</Issue><PubDate><Year>2017</Year><Month>Sep</Month><Day>01</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>KMC 3: counting and manipulating k-mer statistics.</ArticleTitle><Pagination><MedlinePgn>2759-2761</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btx304</ELocationID><Abstract><AbstractText Label="Summary" NlmCategory="UNASSIGNED">Counting all k -mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k -mer databases. Usefulness of the tools is shown on a few real problems.</AbstractText><AbstractText Label="Availability and implementation" NlmCategory="UNASSIGNED">Program is freely available at http://sun.aei.polsl.pl/REFRESH/kmc .</AbstractText><AbstractText Label="Contact" NlmCategory="UNASSIGNED">sebastian.deorowicz@polsl.pl.</AbstractText><AbstractText Label="Supplementary information" NlmCategory="UNASSIGNED">Supplementary data are available at Bioinformatics online.</AbstractText><CopyrightInformation>© The Author (2017). Published by Oxford University Press. All rights reserved. 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